You picked one of the worst 360 controllers to use.
You'll need to isolate all of the LED common from ground, unless that's what you meant, as the PS3 controller uses a Common Anode setup whereas on the CG2 it's Common Cathode.
You didn't need to isolate all of the ground connections, since the [ ], X, O, /\, R1 and R2 all share the same COM2 connection, again unless that's what you meant, but if you isolated them all then what you've done is make it so you'll need to use around 90% more wiring than is necessary.
The Reset (Sync) switch needs to be left connected to Ground like it already is, that's the only button on the entire board that you don't have to change or isolate anything on.
The best thing to do with the miniBoard there (that has the X-tal on it) is to desolder it from the board, then remove the X-tal from the miniboard, insulate the top of it with a piece of tape or something and just rewire it back up with 4 wires to the original spots, but however you go about it as long as it's wired back up it'll be good to go, just keep the wiring for it as short as possible.