there are 2 different pedal setups. 1 setup bolts the master cylinder to the transmission in a little cradle. The other, often found on larger trucks bolts the MC to the frame. Both setups use the bellhousing to mount the brake and clutch pedals.

As you have gone to the darkside by putting in the SBC and auto trans, you will likely have to use a Lokar gas pedal, and a hanging brake pedal setup, so the holes in the floor are moot.

John