I had a really hard time putting it back together as it just wouldn't go back in. You just have to keep messing with it and at one point, it'll just all fit together perfectly.
I've been working on getting the shaft back into the window motor for the 3 hours, to no avail. How did you do it?

 

If you are having a hard time doing it by yourself, I am suggesting you get friend to help you on this one, have your friend to hold the panel while you are holding the motor at the back of the panel, align the holes, and have your friend put the screws back in.

I have just done with the window motor on the passenger side with my Gf, she helped me alot.

 

No problem doing by myself. This morning I took the whole door apart, this time is 10 min. I just can't get the top back on the new motor. I took the top off because the square gear wouldn't line up with the bracket hole. I twisted the shaft until the square matched the bracket, but I couldn't put the top back on. So I gave up. Its 5:15pm and I've been trying since 10am to put the cap back on the motor and it just won't go back together. Lets see if Kraagen will give me my money back. If I can get another motor without being charged (because I couldn't put the top back on), this time I am sure the square gear should line up because most people here have not had a problem with it not aligning. If I run into the same problem I will just power it up and spin it until it lines up.

 

the gear with the brushes?

you have to use a small screwdriver to hold back both sides of the brushes while you slide it over the commutator. It's tricky but very doable. 2 small flathead screwdrivers.