#1
So I built a DIY fuzz circuit, tested it out with alligator clips, everything's good. Did the soldering and boxed it up. When I plugged it into the amp and guitar, I started getting crazy feedback/noise. I have no clue why. It still functions, but can't figure out why I'm getting this awful noise in the background. Anybody know?
#2
Probably bad lead dress. High-gain and high-impedance circuits are sensitive to things like noise pickup and capacitive coupling between adjacent leads.

In other words, stuffing the wiring into a box and using excess lengths of wire can cause high-gain and high-Z circuits to go nuts.

Lead dress practices are one of those things that can't easily be covered in a short post so I refer you to this link. He talks about tube amps, but the basic principles are the same. Google may yield some transistor-circuit-specific info, but you may have to dig for it.

http://www.geofex.com/article_folders/lead_dress/lead_dress_in_tube_amps.htm

Hope this helps, man.