As far as wiring goes, if you're using the stock wiring it's pretty easy too. I think you can reuse the alternator harness but the engine gauge wiring will need to be changed. That's really easy, it just plugs into the bulk head on the fire wall. It's cheap. The neutral safety harness goes from under the dash through the firewall by the gas pedal and plugs into the harness on the trans. The harness from under the dash has 4 wires, 2 pairs. One pair with the black plug is the neutral safety, don't worry about that. The other plug which is red is for the back up lights. Under the dash you can simply reconnect the neutral safety harness from the solenoid wiring portion under the dash, bypassing the trans neutral safety wiring back into the main harness and be done with it. No jumpers, splicing or butchery needed.
The trans cross member will work with either the factory 3 speed or 4 speed. If you go T5, you will have to buy the associated swap trans cross member. Personally I love the Toploader 4 speed. I was going to put a T5 in at one time, it's somewhere in my barn.
I'm not a complete idiot, pieces are missing.