I looked into this pretty extensively when I had my 89 YJ. Another guy on JU actually did it successfully at the same time I was working on mine and I ended up selling him some of my stuff when I scrapped my project.
Here's some stuff to think about.
To make this swap easy and cheaper you may want to consider finding a NV3500 from a TJ. Then get an NP231 from a YJ that had a 6cyl/AX-15. This will bolt to the skidplate/crossmember from a 6cyl/AX-15 YJ without modification and use a stock YJ/TJ clutch assy. You would also need the TC shifter from an AX-15/NP231 YJ. If your Jeep isn't lifted too much you could also pick up stock 6 cyl driveshafts and use them too. All of these are easily available stock parts that will bolt into place will save you from "nickle and diming" yourself to death from the bellhousing back. Think about it, everything you have there came factory in the YJ/TJ frame at some point and it is all bolt in with no fab required. Replacement parts are cheap and readily available both new and used. The only frame difference in your YJ is the motor mounts which you are going to cut off anyways. Bolt on the rest of the 6cyl parts and save the cash for making the engine happy. I considered doing this exact thing with mine before I scrapped the project (due to having to move to NC - not because of roadblocks in the project) except I was going to use the AX-15/231 I already had in my YJ and leave it all stock with the exception of going to the external slave clutch. Since the NV3500 series trannies are currently used behind Jeep I-6's and Dodge V8's from the factory, it would be a better choice plus since they are newer, you can get your hands on a low mileage unit. You end up with V8 power and a reliable overdrive 5 speed using stock pieces.
For the motor, the 304/360/401 will bolt to the stock Jeep I-6 NV3500 bellhousing, no adapters required. All you need is an appropriate AMC V8 flywheel (AMC V8's are externally ballanced so it must match whichever engine you are using) and an appropriate size pilot bushing for whichever tranny you get. You can get exactly what you need from novak or advance adapters for less than a good lunch so why cheap out here. IIRC, they are less than $25 plus shipping. If your 360 came behind an automatic, you may have to remove the ring in the end of the crank where the converter snout seats before putting the pilot bushing in and flywheel on. For motor mounts, you can get ready made, weld in mounts for putting an AMC V8 in the YJ from Advance Adapters for like $150 IIRC. You can fab your own from the stock SJ units that the motor came with if you like. You will find that the SJ frame rails are a bit farther apart (less than 1" IIRC) so you have to make new frame side parts (or modify the existing ones). I looked into this and since either way you end up welding mounts onto the frame, I chose the AA units. They also have bolt holes so you can drill the frame and bolt them in to test fit everything, then weld them in place later to make them permanent. I could not see using old ones with 20 or 30 years of metal fatigue but that's up to you. Once you are ready to drop the motor in, bolt it to the tranny, bolt the tranny into the stock tranny mount location and lower the motor down to where the mounts are where they need to be on the frame rails. You can mark thier locations, pull the motor/tranny back out and then drill the frame for them. Once they are bolted to the frame rails drop the motor/tranny back in and make sure it all fits good. Use grade 8 bolts for the mounts but do not drive the Jeep until they are welded. They are just temporary and could shear off when the motor or frame twists (I know because some one actually did this and had to buy a new exhaust and oil pan when one of them broke and the motor fell onto the front pumpkin on his "test drive"). You can mock up the whole thing just pull the motor after you're done and weld them. It doesn't take but a couple of hours and is well worth it. It also gives you a chance to clean up the engine comaprtment, paint it, and eliminate any extra wires and such that you don't need anymore.
Once the motor is in you can look at all the other things you need as systems. Consider each seperately and you will find things may come out better. Looking at the fuel system, you need to bring fuel up from the tank to the carb. If your YJ has an electric pump setup from the factory, you may be able to use that and just install an inline fuel pressure regulator. The carb on the V8 uses a lot less pressure than the fuel injection. You may have to change the routing of the line and plug the return line but it shouldn't be too hard. Make sure you leave the tank vent line hooked up the charcoal canister so the tank will still vent or you will have problems. You can vent the canister to the emissions port on the V8 and even use the stock V8 CTO switched to trigger the vent signal if you want. You can also just run straight vacuum to the signal port so it dumps when you start it but I am not sure how long the canister would last with constant vacuum on the signal switch. For ignition, I would suggest swapping to one of the aftermarket AMC HEI setups. You can pick these up for $150 and they do work great. All you need for wiring is a key on hot 12v feed for power to the unit (make sure it doesn't drop to 9v during cranking) and then plug your stock tach wire into the other side (if the 4 cyl YJ dist has a tach wire). Your stock tach will need modification to accomodate the V8 but instructions to do that are on the net. You could also use a cheap aftermarket tach and leave the stocker dead. It's up to you on that one. Next thing to look at would be power steering. Your YJ will have the newer style hoses and fittings. The SJ motor you have may have the older kind. One of them uses and o-ring setup and the other uses a flared fitting. You are left with 2 choices here. You can have custom hoses made with flared on one end and o-ring on the other, or you can swap in the steering box from the SJ the motor came from. If the motor donor is new enough, it may have the newer fittings and you would be able to use the YJ box but I can't remember the year they changed them. I think it was around 80 or 81 but I'm not sure. So if your motor donor was newer than the changeover year, your SJ's lines would fit the existing YJ box. For brakes, you just need to make sure you hook the YJ's booster vacuum line to the same place the donor line hooked to on the motor. For the cooling system, the YJ's heater core lines can hook up to the same places as the donor's lines did. You may have to get longer lines as the YJ ones will be pretty short from the 4cyl. A lot of people swap in a 3 core V8 CJ radiator since it is flange mountable like the YJ one. You may have to trim the flanges and opening a bit and drill some new holes but it is much cheaper than buying a conversion unit. You should be able to use stock CJ V8 hoses right from the local parts house. IIRC that is what the other guy did and he mounted his just like I said above. A lot of people swap in an electric fan at this point and the one from the Ford Taurus is quite popular. It's up to you on this one but if you do a lot of water crossings the electric is nice since you can shut it off. There are lots of writeups on the net for this swap.
Had to cut this into 2 posts since the board has a 10k character limit per post...
on hand!
