00 XJ with 95 Motor

My motor took a dive, so I have my hands on a 95. Plans are to swap it in but keep the 00 intake, coil rail, etc and fab up whatever brackets are needed. A buddy mentioned that the PCM from the 00 may not work perfectly with the 95 motor since it will run slightly different. That prompted a discussion if its possible to flash the PCM with different parameters so it'll run better with the 91-95 block. Thoughts?

Any 1990-2001 XJ Cherokee or 1993-98 ZJ Grand Cherokee 4.0 L engine block will interchange.

Remove and re-use ( or replace with new ) as needed or required from your original engine: Intake/Exhaust manifolds, flex plate/flywheel, cylinder head, water pump, distributor-less ignition or distributor assembly, OBD engine sensors, fan belt driven accessories, and/or mounting brackets.

The PCM will not know or care when the engine block was built.

Alright. I figured that since the HO block likely ran slightly different since the internals weren't exactly the same that the sensors may not have enough adjustment to be perfect. If that's not the case, then even better! Thanks!

The 95 is a HO engine. So it should be same. And it should be old enough that it won't have piston problems like a 2000. Guessing yours broke a piston?

The cam stator (replaces the distributor and cam sensor on passenger side) will definitely need to stay with the Jeep. Use the 2000 fuel rail and intake manifold and exhaust manifold.

Coolant temp sensor is different. Also the Alternator is going to have a different connector, so use the alternator out of your 2000.

Crankshaft sensor is different. I'd get a new one from the dealer and put it in while the engine is out of the Jeep. And might as well throw a new flexplate at it too.

A 2000 should have the 0331 head and, if a California spec XJ, would have the two mini-cats.
Either way, the exhaust ports are different between the two engines and the 2000 header will not properly cover the 95's bigger exhaust ports.
Either the 0331 head needs to be exchanged or an aftermarket header, that covers both port styles, is used. Banks Torque-Tube headers do this.
Not sure about other brands of headers.
You could also use the 95's stock header and mate it to the down pipe, if not equipped with the mini-cats.

The computer talks to the electronics not the iron. Move your sensors, fuel rail, ignition, etc., to the new motor and the computer won't know the difference.

The issues you are going to run into are mechanical. Some of it is simple stuff, like the intake manifold and power steering assembly will have to be moved over to the 95.

One big issue is your '00 has coil rail ignition so you will need to fabricate something to let you mount them up--some people fabricate mounts, some people use a remote Viper coil pack and run spark plug wires to the plugs, etc.

Another big issue is that the exhaust ports on the head changed in '00 and your existing manifold won't match up to the '95 exhaust ports. Depending on the emissions package installed and your state and local emission laws, you may be able to simply install an older exhaust manifold. If that's not an option then you will have to either install an '00 or later head (which would also solve your coil rail problem) or you can fabricate some adapters (search).

There's a gasket that you can use when mating the 2000 mini-cat manifold up to the older head.

Thanks everyone!