+1 for getting a wiring diagram!
For engine swaps, the first thing I buy are the manuals for the donor and the recipient. They are invaluable for not just wiring but they usually contain troubleshooting flowcharts.
My first engine swap was a 1991 TPI engine into a 1986 Fiero. Luckily the color codes were very very similar between the two vehicles, but I still spent a lot of time on the floor watching TV with both manuals open and the wiring harnesses from both vehicles spread out.
Also -- don't know if you can still get them, but raid a self service candy or bulk foods shop. They carry (or used to) twist ties with a big paper flag on the end -- very useful to wrap around the wire and label it. Once you have all the wires traced/pinned out, you'll still have to put it on the motor and see which wires will have to be shortened/lengthened to get around the engine compartment and to the ECU.
Good luck! I was only 1 wire off on my first project -- forgot to put 12V to the ECU. Only took about 20 mins to find that since I had one wire with the little paper tag on the end not going to anything (it got tucked into the corrugated loom and not connected).
hth,
-jeff d