I don't see why it would offer any huge advantage to have a new case for the controller. Of course, it can help a bit, but you're bolting it onto the side of a motor, that is operating well above it's rated power and that motor will get hot if used hard.
12 good mosfets can reliably make 40A or a little more. The standard fets in the HD, are nothing special. Swap them out for fets with about half the resistance, add an extra shunt, and I'm guessing plus 50% should be fairly reliable, so long as it isn't pushed really hard, for a long time, with a big battery pack
The mod isn't that difficult to do, but getting it right, first time, without wrecking it, isn't so easy.