I have two cross members, my '88 and a '91 or '92. They are different. The '92 is sunken were the tranny mount is at. I think the original '88 cross member is the way to go and drill some holes in it. I'll cross reference the tranny mounts between the TJ and XJ.
On the motor mount brackets, I had to cut off, reposition and weld one of the ears. I think it was the drivers side. The other side, I made a spacer. I felt it was a better option, than risking messing up the block. I also try and modify the least expensive or easiest replaced part. I have an '88 engine, a '95 engine, a 2000 short block and the '03 engine. The motor mounts from the '88 fit the '95 and '00 blocks. I did run into someone who had problems with a newer block not fitting a YJ or TJ. I think it was 2000 block out of a Cherokee. I didn't get details, so I can't say what the problem was. I bought the '95 block off of him. I used the head off that engine for the motor in the '88. I do have the motor mount brackets off the 2000 motor. They are virtually the same as the '88 motor mount brackets.
Tom
Edit: The motor mount brackets are cast steel and not cast iron. The are suppose to weld fairly easy. I had a local shop do the welding. I think it was $30-40. The 2000 brack has an elongagted slot on one of them, where as the '88 just had a hole.