My car is an auto-manual swap as well... The clutch pedal that PO had in there was way over like that too... What I did was get a different (JDM) pedal set off Ebay where the clutch pedal didn't have all that clutch safety switch crap on it (not needed for the swap)... Now my pedals are close together; and nowhere near the footrest.
Before:
After:
Aside from that, modifying the pedal is really your only other option.
GL!