Like others before have said, the odds of it slowing down because of a bad mod are next to none. A bad mod will just result in it not working. Also be careful about your solder, especially with those nice crimp quick disconnects from lizard lick. Crimping it bad will cause you to drop inputs as it doesn't make a decent enough connection to the disconnect. This has happened to me right in the middle of a tournament and it was not fun. Made a point to solder everything but quick disconnects to buttons after that....
If you're afraid of messing up your TE/SE board, solder the inputs to the terminal block rather than to the board itself. If you want to tap into your USB, best idea would be to cut and strip a decent amount of usb wire to connect to your custom PCB like a MCthulhu + Imp, Dual strike, ChImps, etc... That way you can take the part about fucking up your pcb out of the equation. Just make sure you dont' cross any of these usb wires when you do attach them to the custom pcb. Especially DO NOT CROSS YOUR RED WIRE AND BLACK WIRE TOGETHER unless you want a fried console. Always test out your mods on PCs before you do it on consoles.
Happy modding~