At least the thread starter is beginning with large-enough cases.
Some of the older joystick cases have marginal room — even for replacement PCB’s as small as the MC Cthulu let alone putting in an XBox 360 PCB!
I wouldn’t recommend trying to put an MC Cthulu in a Hori Fighting Stick case or Namco case myself. Those are very marginal. I only tried to prep a legacy case for the MC Cthulu AFTER I’d done at least a half-dozen mods before that and got used to my cutting and filing tools.
I gave myself the task of prepping an Agetec case for MC, myself. There was a LOT of plastic cutting involved there and quite a bit of it had to be shaved and filed down by hand because of the space restrictions. You just can’t use power tools (Dremels with cutters and sanding barrels) for 80%+ of that work. It was a huge job making room for the LS-32-01 in that stick.
As for what I’m doing with a Round 1 TE PS3 case, that’s a different story… Huge amount of room to work with once you take the case completely apart. (It’s easier to do than most people make it out to be… Just be sure to keep all the screws in Zip Loc bags so that you don’t lose them!) After you remove the original Mad Catz PCB’s and see what you have to work with, I don’t see that there’s much you COULDN’T fit inside that case!