Great idea on using the pedals as a drilling template! You're right, the drill bit does want to wander on the brake and clutch, and your method would allow for easy drilling on the outer corners. (I assume you used something like cushioned workworking clamps or cushioned a C clamp to avoid marring.)
RE: throttle, I did not actually remove a "cover" (note to self, do not write DIYs late at night on three day weekends.)
Did you find the clutch pedal was plastic?
Thanks for the tips--this should make it easier for others to get excellent results! I like your decision on the screw locations better too (so does the supervisor).
DIY has been updated with your improved information and corrections. Nice work!