Gut the Gameboy if you did not purchase a 3d printed version.
Cut excess tabs (not the screw holes!) to free-up room. Save the main board, you can still use that.
Cut the main board in half ware you can still use the 2 pre-drilled screw holes to mount the board. Make sure you do not cut off the button contacts. You will need those as placement for your buttons.
Drill holes for the buttons, Thea heads should be poking out.