As much as a manual swap would be nice, it's not really worth it. And the auto windows actually are nice, especially on the passenger side. Nothing like leaning across the cab to try to roll it up or down in traffic...
Just do what I do:
1. Remove the inner door panel(plastic).
2. Using a drill, drill out the 4 rivets holding the entire regulator assembly to the inner door frame/panel.
3. Carefully wiggle out and remove the entire regulator. You will have enough room to get it out through the upper hole in the door panel, once you remove the "brace" that covers it with 2 screws(this is what the door closing handle/arm rest screws to).
4. With the whole thing out, replace the motor. 3 screws and $30 and you are done.
5. Take 4 1/4-20x3/4" bolts and nuts. Tack weld the nuts to the back of the regulator(where the original rivets sat). You'll do this by putting the bolt in from the door side of the regulator, put the nut on and tighten it down... on the workbench. Now, just tack weld that nut, then remove the bolt.
6. put the regulator back in the door and into place. You can now just get one of the nuts to line up, put your bolt in from outside and get it finger-tight. rotate the regulator until another hole lines up and do the same thing. Install the other 2 bolts and tighten it down.
7. Reinstall door panel.
As much work as that might seem, it's still maby an hour's job if you have the tools handy. You could probably omit the tack-weld step, but I'd do it, even if I had to use a 12V battery, jumper cables, and a stick of metal to just get a cruddy tack.
Now, you can do the replacement again in just a few minutes, as it's only removing the 4 bolts and the whole thing comes out.
edit:
Also, pretty sure that replacing a door is actually more work than doing this.
I've done both... and the replacing a door is a real pain. Very little clearance for wrenches and sockets to get to the door bolts, and once you get it together you have to adjust it until the door closes - 2 hinges, in and out and front-to-back, up and down. It's a bit of work, that's for sure.