The injected 4.0L didn't replace the carbed 4.2L, they were used at the same time from '88-'90, the FI 4.0L in the XJ/MJ and the carbed 4.2L in the YJ. It was in '91 that the YJ adopted the FI 4.0L already in use on other models and changed the Renix system to an updated more reliable MPFI system.
The Chrysler 4.0L used in jeeps was never carbed.
You can use a 4.0L head ('91+ HO) on a 4.2L for a great power boost, so it stands to reason that the 4.0L intake and FI will adapt as well. The intake runners are higher on the HO head so you'll have to use large washers on the manifold bolts to hold everything on.