If its a vtec engine you'll need to run wires for:

vtec selenoid (1 wire)
vtec oil pressure switch (2 wires)
heated o2 sensor (3 add'l wires - i opt to turn mine off with crome)
and youll need to preferably make a jumper for the obd0->obd1 dist plugs.

This is assuming you use a plug-n-play obd0->obd1 harness like i did. its piece of cake.

As far as MPFI, dont even think about swapping engine/dash harnesses, its REALLY not worth the trouble lol MPFI is a piece of cake, yank the entire engine harness out and run your mpfi & obd1 wires at the same time and re-tape it up. Ive done quite a few engine harnesses. I keep a few extra plugs laying around so I just add 1 additional connector at the passenger shock tower so the harness still can be disconnected like stock.