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).