Well I went for a test drive after putting on some new rear brakes that don't work, and noticed my tranny clicks in 1st gear. Its more noticible between 2000 and 3000 rpms, but it clicks throughout all rpms. However, as far as I can tell the clicking is only in 1st gear, when I shift to 2nd it goes away... Is there some kind of 1st gear bearing that could be going out? Or is it another kind of problem? The clicking also varies with rpm, faster the rpm, faster the clicking.

 

I'm guessing no one's see something like this...

 

Partner, I had a similar issue w/ my 97 Tacoma slushbox. The problem "clicking" was coming from my rear drums. If you didn't notice this before changing the brakes, the greatest possiblity is that your click is merely coming from putting your truck into gear and the slack coming out of the drivetrain from bad u-joints. Just a possiblity...if not that maybe your brakes.
Good luck.
-Chad