Argh. I was just saying yesterday that these "universal" aftermarket wiring "solutions" (e.g. from Painless) make the hair on the back of my neck stand up and do the creepy-crawly. Stuff like this phantom shorting happens and because the wiring is poorly documented and poorly supported, you're left totally on your own.
You'll have to start by pulling all of the individual-circuit fuses and putting them back one at a time to see if the main fuse blows. If not, then you'll have to disconnect all the feeds between the main fuse and where it branches, and reconnect them one at a time until the fuse blows.