Nice that you got the two motors, How long have they been sitting?
I've been trying to organize my pictures of my project but unfortunately my stupid macbook's screen blew and I'm going to have to either replace it or find a way to get in and get my pictures off to my PC.
I'd advise not getting too heavily invested too quickly, I'd start by pulling the head, inspecting the cylinders for anything unusual, look at the bottom of the had, and slap new gaskets and belts all around. (Oil pan, Head, Valve.. etc). It can get costly very quick. I'd slap some belts on it get it timed up and get it running well. Take it from there, determine if it is something worth sinking your teeth into or not. I really wish I could start a thread of my own now, but I really need to get the pictures first.
This is going in your 94 right? Because that is the same year I'm swapping the one I've been working on into. I'd also hang on to your spare motor at least in the short term, then part it out after knowing you have all that you need.
I also want to put you at ease with wiring. It sounds like your pretty nervous about the difficulty. Like snoranger said, there isn't much too it. I actually found it easier to make my own harness and integrate it with the stock harness. Much of it you don't need, and can be removed. Keeping the bits and pieces that run the lights, or the reverse light wires for the trans.. etc need to stay. You need one wire to the injection pump, and a wire to engage the starter. Thats it. EASY! Just use proper relays and fuses and you will be golden.