The 2.9l and 4.0l OHV share the same block so mounts and trans bolt pattern are the same, just a straight swap.
Fuel system is based on the year, fuel injected before '97 run 40psi with return line, '98 and up run 65psi with no return.
You do need 4.0l computer and wiring harness for the swap, and computer needs to be for automatic or manual trans, which ever you are going with.
Computers are also matched for EGR valve and Cam Position Sensor.
Best bet is a '90-'94 4.0l with it's computer and wiring harness
'95 was the OBD 1(EEC-IV) to OBD 2(EEC-V) computer transition year, and will add another layer of complication.
Good read here:
http://www.therangerstation.com/tech_library/4L_Conversion_faqs.shtml