Swapping harnesses isn't difficult but it is time consuming. Do you have all the harnesses from front to back?
You can replace EVERYTHING with your 01 harness and be 99% plug and play...plus able to get a crawford reflash, etc. (bulkhead harness, engine harness, fender harness, tail harness.) If you're missing any of the harnesses...you can still make it work but you will be doing more splicing. Keep in mind if you are going this route and are avoiding wire splicing you will need to use the newer style dash...or at least new-style cluster to plug into. This is also nice because when you're done you can plug in a OBD II scanner and read codes if you have issues. Donor car is best for this route.
Your other route is much easier and cheaper but slightly less fun. You can run the 2.5 with the 1.8 ecu. The car take a few more rpms to get going on the low end but it will run fine. You also will not be able to get a reflash with the older 1.8 ecu.
Either route above should hit your goals: "easy to find parts, good gas mileage and wicked reliability"
Do a bunch of splicing and merge the 93 harness with 01 harness. Still not rocket science...but may be less reliable or harder to trouble shoot if you are not skilled at wiring. This may put you in the same mess you are in now where you aren't sure of your wiring situation.