I have a 2004 SR5 and I was experiencing the same problems as most of the members, window not working, wiper and defroster working fine. After reading the forums, I did some troubleshooting of my own, relay's, fuses, etc. All of which were fine but the window issue.
I was about to click the purchase button on
ebay for the OEM motor and I held off. I couldn't help thinking that I might have to purchase both motor and rear ECU.
SO I did some isolation with a test light and found that the ECU was working, by checking the electrical path that powers the motor. See the motor is grounded to the chassis, so the electrical plug just tells the motor to go one way or the other (polarity).
In doing so, I stuck the pointed end of my test light into the power plug coming from the ECU and flipped the switch up and down, causing the light to come on and off, vice versa in either connection.
After plugging the socket back in, the window worked. I don't know exactly what I did, but shoving the test light into the plug from the ECU, and reasembling.
So my issue, was that the connection coming from the ECU was not giving the motor power (apparently). After putting it all back together, it has worked fine now for about 6 months.
Can't hurt to try then spending 100+ dollars replacing parts that aren't broke!