84 mustang with 2.3 from a 91

Your 84 is carb? If so, that would not be fun at all.

Yes, the engine wiring harness can be removed from your 91, but not without a lot of pain. The computer is to the right of the passenger foot area, with most of the wiring harness going through the firewall there. My only suggestion, is label each wire as you disconnect it, or you will be very confused.
 
See the thing is the 84 has no engine so i am putting the 91 engine in there is there wires that have to be cut or is there anything in particular i need to watch for??
 
I'm not sure exactly... but I'm betting this car was originally a carb car... thus you'll probably want to swap the fuel tanks with pumps and the fuel pump relay/wiring too.

Otherwise, the main thing will be to make sure you reconnect all the wires on your engine wiring harness so the computer can see all the sensors.