Jeremy,
You can have the stock A/C and Heater box in a Stage II car if you are using Champion or TA stage 1 type heads and not Stage II heads.
Things are a bit tighter, i think because of the heads maybe being taller AND using the taller valve covers, but otherwise, the engine is dimensionally the same as a stocker.
My car, in particular, has all of the stock stuff, but has a piece of the bottom most corner of the heat shield cut out to clear the valve cover better. You can't even see where I cut it.
The would be a lot easier to work out without A/C though... there's a give and take to everything.