Two things - Typically, on a power brake car the brake pedal sits a little lower than the clutch pedal. This is true accross the board.
On '65 B-bodies, the brake pedal is longer than on non-power applications. The pivot point is mounted higher in the brake pedal bracket. If the car was PB when it was auto, you should be able to see this. It might also make a difference.
(I have a Auto PB set-up in the garage if you need a picture of what this look like.