Play Smash Run relentlessly.
Dang it Sakurai!
My advice would be to either play Crazy Orders or Trophy Rush consistently (the latter will net you customs for the particular character you're playing).
This can drain your funds pretty quickly, though, so an alternative is to play All-Star. Custom bags appear in the rest area between matches and you can get a good handful of them if you clear the mode. They appear regardless of the difficulty setting and you won't lose them even if you're knocked out - ergo, you can just hop in, win a couple of rounds, grab your goodies and SD in the next round. It's probably better to just keep playing on anyway, as you get more rewards the further you get, though it's up to you how you want to do it.
Note that there's every chance of ending up with custom equipment as opposed to custom moves, in addition to customs being randomly generated. There's really no convenient one-stop solution to getting customs quickly, and any way to go about it will still require consistency and patience. Just keep at it. Finding them as you play over time will eventually get you everything.
