to revive an old thread for the searchers.
the intake manifold was different. apparently the power steering pump was different, and the bolt pattern for the power steering pump on the intake was different. it was a really easy swap to change the intakes.
the fuel rail is different, the YJ had a return line, the XJ had only the inlet. came along with the intake swap. there vacuum lines coming off the intake were different too. the yj manifold had 4, the XJ had 3. just had a plug in one that is removable with a 1/4" rachet.
there was an extra pully on the YJ block, near the alternator. i just set the belt to the top of it and had no problems.
that is all i found, i was driving the jeep today, and passed emissions. good luck with your swaps! and bump this thread if you feel it was helpful.