As i am getting ready to swap in my new motor from a 97 TJ into my 89 YJ i pretty much have everything figured out but someone told me that the newer motors have a different CAM profile and that the newer camshaft wouldnt work well with the 89 EFI setup?? (I am using my old EFI and just swapping block and head from the 97 due to time and $$)
Is this true? If so, what causes that?
Other than that, piece by piece the motors are damn near identical.
The only way in which a camshaft profile will affect an EFI system, is if the cam demands more fuel than the injectors can phisically supply. The factory EFI systems are made to run with the stock cam, but they have a bit of "self adjustability" built into them. The Oxygen sensor (make sure you use the O2 sensor from the '89 system, it may be different than the '97 unit in info delivery to the computer) will see a lean/rich condition and tell the computer to adjust fuel flow/patters accordingly.
If you were going to put a cam with a larger (more lift &/or duration) profile, it might be a problem, but a '97 cam and a '89 EFI system shouldn't give you any problems.
Just a note, I haven't done this swap, but have messed around with aftermarket cams in stock EFI setups and have had good results using mild/RV type cams with NO problems.