K well I ordered it hah

 

Ok, I did this research just in the nick of too late.... I'm doing essentially the same thing as you - swapping an engine from '96 ZJ Auto to '96 XJ Manual.
The ZJ engine came out OK. The XJ had the external !@#$%^& Torx bolts holding it on. Bought a set of sockets in order to get the one E12 I needed.
The ZJ engine has all different electrical connectors - so I need to swap out all the sensors, camshaft position sensor, and throttle body.
The dealer told me the Auto trans uses the same bolts to hold the flexplate on , as the Manual uses for the flywheel - WRONG!. The bolts are 1/2" fine thread, but for the flexplate they are 1/2" long, for the flywheel they are 7/8" long. I got some grade 8 bolts 1" long, but they stick out the back, I'm worried they may interfere with something (probably not..), so I'm going to reuse the bolts from my donor engine. (Can't use washers under the heads, or they will interfere with the clutch plate).
And then I run into the problem you have here - the adapter for the pilot bearing.
I pulled the pilot bearing out by using a long 5/16" carriage bolt - stick the flange in behind the pilot bearing, jam another 3/8" bolt in the hole so it can't escape, and slide-hammer it out. Leaving the adapter in the hole. No space in behind the adapter, so my improvised slide-hammer can't work. This is my DD, I need it on Monday, I can't wait for parts....

Finally, the whole point of this post: I managed to extract the adapter, by drilling and tapping two holes in it, then pulling it out with a couple 1/4" bolts through what I call a strongback.
The metal the adapter is made of is not too hard - tapping worked OK. The proper tap drill for 1/4-20 is a #7 drill, I don't have one so I drilled it 13/64 (I think). I had help to make sure I was drilling straight, 2 holes opposite each other. Now I'm happy, gonna assemble it up tomorrow and hopefully have it running by suppertime.

 

I had to goto the dealer and order a set of grade 10 bolts for the Flywheel when I broke one off.

There is two different pilot bushings, the BA tranny has a smaller diameter input shaft than the AX-15.
So when you get it, make sure it will slide on the tranny before driving it into the crank.

Took me some trial and error to get the correct pilot bushing/bearing.