05-06 are kind of oddball years for engine management because they are the only two years which used the NKG engine management system.
97-04 models used the Chrysler JTEC setup.
I'm going to go out on a limb and say it will probably be easier to use the 2000 sensors/harness/ECU if it isn't CAN bus like the 05-06. Otherwise you are going to have a lot of little wiring issues to deal with, some of which might not be readily fixable. That said the 05-06 4.0 makes slightly better #'s which some folks attribute to the more advanced NKG computer, all other mechanical parts being identical to an '04 except the oil pump drive, who's sensor is specific to the NKG vs. JTEC previous.
'94 YJ - SBC/AX15/231, SOA, 8.8, 34" swampers
'06 LJ Rubicon - 31" ATs, OME 2.5", belly-up skid, other junk
'75 CJ5 - 232/T14/D20, 'glass tub w/ 2" BL, otherwise stock