2 part question. pro parts headers and A/C heater box.

I am building a low deck for my 70 swinger. The car has A/C. I removed everything but the heater box. Will the engine fit with the A/C blower motor, or do I have to get a non A/C box?
I will be running pro parts semi fenderwell headers. I have heard they aren't that great on a low deck?? Any info/tips are well apricated! Thanks!