First hand experience here...
Just swap the long block into the 90. Swap the 90 intake, exhaust and front accesory drive parts onto the late model block and head. Swap your distributor and motor mount brackets as well.
I just finished doing this on my bro-in-laws 90 XJ.
You will need to run the temp sending unit into the thermostat housing. The 90 has the port for this on the drivers rear of the cyl head. The 99 will not. Drill and tap an 1/8" hole in the t stat housing and screw the sender into it. Aside from that it is a bolt in swap.
You will end up with a 99 4.0 with 90 XJ Renix injection installed onto it.
