Hmm, well, the easiest thing if you're certain the controller is at fault, is to just buy a replacement controller. It will be <$40 from the right places. Second easiest place is salvaging from a broken scooter of similar power; frankly that's also probably ~$40 off of craigslist. + You'll have a bunch of other good parts. In either case, unless you get a perfect replacement, it will require figuring of the cables and maybe splicing a few. I assume you can use a soldering iron.
But, i would try to look up "troubleshooting brushed scooters" or something like that. It would be nice to increase your confidence that it's actually the controller, before splurging on any new parts.
And..yeah...the whole drawing 24v from the pack would not easily draw evenly. You would have to draw from one half of the pack, then draw from the other half for an equal amount of power, and then balance them all every time. Would be more complicated and pretty annoyingly useless.
New to endless-sphere? Notice a lot of signatures recommending Ebike.ca? That's because it's the best place for a quality and manageable, (but still 'real'), first build. Justin is a solid supporter of electric bike development, and a good source of equipment.
My hat off a thousand times to the green people that effectively run this forum. The ES Mods are superb.