I haven't posted on this site in quite awhile, but I felt like I needed to give something back for the great info I've gotten off of here - in particular Brandon's great gsr swapguide.
I did my swap last weekend and found a few differences from his guide (JDM gsr into Civic Si) in swapping a US B18C1 into a non-B series Civic, which I think I've covered in this swapguide.
This is the target. A 2000 Civic EX with a stock d16y8 and 187,xxx on the clock:

And this is the engine. An iron block Ford 302:

Just kidding. Actually, I'm swapping in a B18C1 from a 2001 Integra GSR. The transmission is from a 99 Si. The reason I'm writing this guide is because in prepping for this swap, I found that no one had written a guide on a completely legal OBD2B swap for this engine into a non B-series Civic.
Here is the motor in the back of my CRV as I originally bought it. Thanks to myhatch98 for a great deal. He's truly a good seller:

The first goal was cleanup. I used a die grinder with a wire wheel on the block, and a dremel with a wire wheel for the tight spots. The tranny, I just pressure washed. I also took the time to paint the valve cover using wrinkle red Rustoleum. It looks good in person, but if I do it again, I'll spend the $$ and get VHT because I think the color is a little better. Here's the result:

Next is to inspect the timing belt area. To do this, you have to remove the crank pulley, which is fairly easy if you have a 650 ft lb impact. Otherwise, keep trying, and it should come off. On my motor, I found that the timing belt was brand new, so I didn't touch it. While you have the timing cover off, you need to replace the motor mount on that side with a B series Civic mount. Luis provided me one from an Si. The top part should look just like the top part of the d series mount, but it is different inside the timing cover.
Time to look at the clutch, flywheel, and pressure plate. I found that the clutch and pressure plate were completely toast, as seen below:

Before installing the clutch, make sure to grease the throwout bearing, shaft, and fork to avoid the notorious Honda clutch squeak:

Also, while I had the tranny off, I replaced the axle seals. They pry out with a screwdriver, and you can press them back in carefully with a large socket and a hammer. They come impregnated with grease, but I greased them again to keep them from overheating and leaking on first drive before the oil starts to cycle through the transmission:

The flywheel was good, so I had a machine shop resurface it for $55, and it looks great. Remember to install the pilot bearing before you install it - if you're replacing the clutch, this should be provided. When you bolt it on, use a cross pattern. I believe the proper torque is 70lbs, but someone can correct me on that:

Then, put on the clutch using the (hopefully) provided clutch tool. I used an OEM replacement Exedy clutch kit. The pressure plate goes on next, and came with the clutch. Make sure to clock it right and torque it down. I don't remember the proper torque for this, but it should be in the manual.

Next, onto the AC bracket, assuming that you're keeping air conditioning. You could probably use the Integra AC compressor, but I wouldn't recommend it because the hoses are clocked differently, and look like they would be a pain to install. Instead, I purchased a CRV AC bracket from Majestic Honda. The CRV is a B series engine that uses a D series AC compressor, so this bracket is perfect, and also cheaper than a DelSol bracket:

Next, put the engine and transmission together. I highly recommend having help. Also, it's much easier to get lined up if you remove the intermediate shaft first. Before you do this, make sure that the dowel pins are in the correct locations. In my case, I had 2 dowel pins trying to share the same hole - 1 stuck in the engine, and 1 in the tranny. It was a bitch to get out, but I sprayed it with PB, threaded a big bolt onto a big strip of steel, and drove it into the center of the dowel pin. Then I could hammer on the steel until it came out. Here's the whole thing together:

Now is a good time to plan. Go over everything that's coming from the Integra, and everything you're keeping from the Civic. I went through my Civic and labeled every plug and vacuum hose I could find with masking tape, and this made it much easier later.
Now, you start taking the Civic apart. Jack it way up and support it on sturdy jackstands. Remove the wheels and splash shields. You will likely break a great deal of the clips. I recommend replacing them with GM clips, as they look identical to the Honda ones, but are way easier to get out later.
Next, remove the cotter key and castle nut from under the lower control arm. Then remove the bolt that holds the bottom of the fork together (don't remember what that's called). The proper way to remove a balljoint is with a pickle fork, but we found that you can pound the hell out of the lower control arm with a hammer, and it will come apart:

Next, remove the axle nuts. Remember to pry out the lock crimp. We still could not get them off with the 300ftlb impact, but they were no match for the Hammer of Thor:

Now, you can move under the car. Undo the shift linkage and header. We ground the bolts off of the header because they were rusty. Drain the oil, transmission fluid, and coolant.
While that's going on, someone else can work on top, removing the top header bolts, airbox, vacuum hoses, plugs, and misc. Power steering pump needs to come out, but you don't have to drain it if you're careful with the hose and jam it behind the reservoir. Then, undo the AC compressor. You don't have to vent it, just lay it to the side on a fender guard like so:

Eventually, you'll have everything done but motor mounts. Now is a good time to support the engine with a jack under the oil pan. Then, you can undo the motor mounts. We did the far front vibration mounts first, then rear, then engine side. Then we hooked up the chain as we removed tranny side mounts. After that, then engine should come right out:

Note: it is easier to get it out with the hood removed, but not necessary if you have someone hold it straight up which you're removing the engine. Now, we install the d16y8 in the Mustang:

just kidding.
Obligatory empty engine bay pics:

Now, take inventory again. while you have the engine out, swap the FPR hose in the car with one that's approximately 8" longer. Believe me, it's much easier with it out, and will need to be extended. Now's also a good time to remove the plastic wire loom that routes under the intake manifold and replace it with plastic tube/high temp tape, as there's no good place to put it on the back on the B18C1. While we were here, I also ground off a small spot of rust from my crossmember and sprayed it over with Rustoleum.
Time to rock. Since the B18C1 with tranny is wider than the d16, it will not clear if it's level. So, chain it up with the engine side about 6" higher than the tranny side. It should slide right in, at which time, you can catch it on the jack and shift the chain so it's level, which makes it much easier to line up with the mount points:

I highly recommend bolting up the rear mount first, as it's an absolute bitch to get lined up when the others are bolted down, as we found out. Make sure that your bolt is not going through the rubber on the mount. Then line up the holes on the other major mounts and bolt them down. Finally, do the vibration mounts on either side.
Next, you'll need to do some wiring. Contrary to what a lot of people told me, you DO have to swap the dizzy plug over on at 99-00 Civic because the Civic has a 10 pin plug and the teg has an 8 pin. Luckily, the wires are the same. You will also have to extend the two plugs under the dizzy (I believe they're both vtec). You'll have to extend the Evap purge valve plug, which was on the fuel rail on the Civic, but is on top of the IM on the teg.
To do all wiring, we used butt connectors with heatshrink tubing, then plastic conduit, then automotive tape over it.
The Civic dizzy plug:

I believe we also had to swap the CKF sensor from a 3 wire to a 2 wire, or vice versa. I honestly don't remember.
An example of Nick's badass wire wrapping skills:

You'll also have to run a wire to run the secondary butterflies in the IM. Since I haven't done this yet, I can't tell you exactly how to do it, but it's just running from 2 pins in the ECU to a 2 pin plug on the IM. Once I get that done, I'll add it to this. If you want to skip this, remove the vacuum hose from the butterfly port and plug the hose. This will cause the butterflies to stay open all the time. If you don't, they'll stay closed, and your IM won't flow as good above 4400 rpm.
You may have to extend other plugs and things depending on your setup. If you're lucky, you can get an entire Integra engine harness to work with (which I had) and makes it a lot easier.
Bolt up shift linkage, and then look at header. The header is going to be about 2" short, and the flanges are clocked backwards from the ones in the car. Nick came up with an ingenious ghetto solution that doesn't leak and works surprisingly well, but I'm going to have an exhaust shop fix it when I get the chance.
The problem is that the civic flange goes from lower left to upper right, and the teg flange goes from upper right to lower left, so the bolt holes don't line up. I used 2 4" strips of steel with holes drilled where the flange hole were and bolted everything together. No pic, but it looks kindof like this:
:0:
Here's Nick screwing with it:

Next comes the really tough part of this swap. The OBD2b Integra ECU has
a built in immobilizer that disables the injectors, and the car will not start. You have a few options: you can convert to OBD2a or OBD1, which would make it illegal in many places if you have to pass emissions. You can remove the immobilizer, which will cause a CEL for Internal ECU Malfunction, but doesn't cause limp mode, and the car will run fine. This will also not pass emissions in most places, but will run fine.
That's what I've done for now, but I'm not going to detail it here because of potential for abuse by thieves. The only legal option is to remove the immobilizer and solder in a dummy chip that makes it run normally. I don't have a source for the chips, but they're around, and there is someone on H-T who will do this fix for like $100. This will be my long term solution, I just haven't done it yet.
Another strange side effect of removing the immobilizer and not replacing it with a dummy is that you HAVE to prime the fuel pump everytime you start the car, or it will not start. When you turn the key over, you just have to wait like 4 seconds before turning it to start. Other than that, it runs fine.
Swap over pins A15 and A16 on the ECU plug for the fuel pump. You should have about everything done now. Add fluids, put together anything you haven't done yet, and start 'er up!

Impressions:
It's like night and day compared to a d16y8. It will burp second, and sometimes third. Much easier to drive in traffic, and needs much less shifting. Clutch is much lighter, and shifter is notchier. The b16 transmission is almost comically short, and cruises just above 4000 rpm at 70 mph. This is a car that I've driven for 6 years and 180,000 miles... I was tired of it, and seriously considered trading it in, but no longer. Definitely worth the cost IMO.
Problems so far (other than already mentioned):
So far unable to get an OEM intake that fits acceptibly. Currently using cut LS arm with d16 airbox and dropin K&N.
Need to T off a vacuum hose to get cruise to work. Will probably do this when I get the secondary butterflies hooked up.
I'm not really happy with the teg throttle cable - just doesn't seem like it fits quite right, and the gas pedal is a little sloppy, even when it's tightened all the way. I'm probably going to throw some washers on the pedal end of it to get a bit more adjustment out of it.
Problems with coolant leaks from using teg hoses on d16y8 radiator. Use GOOD hose clamps, and tighten them as much as possible.
Swapped junk shifter that came with the motor - it was either cut or broke off at the last 2 threads. Today, I found that the B&M from my D-series works perfectly on the B-series shift linkage - shifts like buttah.
Prices (so you'll know what to expect):
70K mile B18C1 with Si tranny, plus mounts/P72 ECU/bad axles: $2080 picked up from an H-T member.
Exedy OEM clutch kit: $90 shipped from Ebay
Resurfaced flywheel: $55 from a local machine shop.
Remanufactured axles: $100 from orly's with core return
Fluids/oil filter: $40
CRV AC Bracket: $75-ish from Majestic Honda
Tranny seals: $15 from Majestic Honda
Assorted vacuum lines/heatshrink/wireloom/solder/butt connectors/: $20
Total: $2485
Thanks to Luis (H-T user myhatch98) for giving me a great deal on a swap, and Nick for providing all of the real know-how and ingenuity when we ran into trouble, plus doing a hell of a lot of the tough wrenching.
When you're all done, :beer:
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