None of the transmission or any of that stuff matters. The axle is the axle, and it will have a flange yoke. I would recommend changing that to a fixed yoke, which ECGS sells. I actually have one that I bought from them and never used, if you are interested. That is not why I recommend you get one, I recommend using one regardless because the flange yoke is sort of a weaker design. Not because of the flange pinion, but the flange Yoke that the driveshaft has to use which bolts to the axle's pinion flange yoke. They are not really designed for the use that an offroaded Jeep may see.
On the 8.8 I would plan for new brakes. I would also plan on new brake lines, I don't remember for sure but you may need to relocate the diff breather. I've read that it can be at too much angle for Jeeps where the pinion needs to be raised, and can start venting out fluid if tilted too much. Common solution is to plug the old hole and drill and tap a new hole more vertically.
Not really a lot of "tips" to give, it's pretty simple in a YJ seeing as you're just installing shock mounts and spring perches to get it into the YJ. Just make sure you decide on a driveshaft (SYE, double cardan shaft, etc) now, so that you can set the axle up for life. Don't want to set it all up for whatever you have now, then change your mind later and have to redo it.
Are you planning a regear? Or are you doing this to allow yourself to do half a regear? I remember you talking about 4.10 and 4.56 the other day, curious what your plan of action is as of right now.
I was going to do an 8.8 for a YJ so I actually have a few parts if you're interested. I have a Detroit TrueTrac, an ECGS yoke, and a crush sleeve eliminator spacer from Ratech. All parts are brand new, I bought them in anticipation of going the 8.8 route and then later a dana 44 fell in my lap so I ended up not using the parts and still have them.
