Car one: 96 XJ 4wd I6 4.0 HO (auto)
Car two: 95 YJ 4wd I4 2.5 (5 speed)

can XJ powertrain go into YJ? Can YJ go into XJ? Does transfer case have to swap or can it stay? Is it even worth my time swapping them?
If so, how do I measure for a custom driveshaft... because I know that’s gonna change
So many questions... so little information...

 

Doable, but you would have to transplant wiring harnesses, engine and trans computers, etc. Motor mounts and mounting holes on the block might be different. Trans mounts would probably need to be custom as the XJ and YJ had different auto transmissions. Lots of headaches and issues to work out, enough that it's not really not worth the effort in my opinion.

 

There is an engine interchange sticky at the top of the forum. Worth taking a look at it.

 

So big a project and not worth it.

It falls into the category of "if you have to ask, it's not for you."

 

It definitely seems easier to just figure out what's wrong with the particular vehicle you want to get running and just deal with that.

I had a 2000 TJ 4.0 5spd with a blown transmission but a solid engine and acceptable body that had a variety of minor issues when I bought my 95 XJ 4.0 5spd and even with the same size engine and transmission type, there were few parts from the TJ that I could use on the XJ. I could have kept the TJ around and if anything happened with the engine on the XJ put the transmission from the XJ into the TJ, but the engines are incompatible so I sold the TJ to a buddy who had the time to fix it up.