So I just got my motherboard back today from repairs. I set everything up just fine. I noticed there are some switches on the top of my case (I think they control fans or something), and I flipped one, which caused something to pop and reset the computer. A little bit of smoke and a strange smell came off the case, but the computer proceeded to boot with no issues. I took a look inside and saw no discernible damage. Fans all work still and the smoke was a little too far from the PSU for it to be that. I suspect and hope that it was just the PWM controller for the outside fans. I probably hooked it up wrong. But that isn't a big deal because the fans are all really quiet to begin with.
Any other theories?
PS: the mysterious popping was the last straw; I have decided I won't be building a computer in the future. It doesn't save enough money to be worth the hassle. Too many things can go wrong in a custom build.