you didnt label them?
If you pulled the trans with the motor out of the top--inspect carefully the front seal in the trans--i know i know it is boted on etc--but you may want to replace that seal--its cheap and if it leaks when you reinstall then it is a lot of work to get back to it..
The harness will actually be kind of start up--kind of hard to get it messed up if you pay attention--the tricky part is getting the fuel injectors hooked up correctly on the harness. It is easy to get them mixed up.
The vacuum lines etc --too much to type! particular ? i can help. You need the manual really.