Auto/Stick
 

If I were to purchase an automatic FC could i still use it for a LSx swap and throw in a t-56, or does the auto tranny screw everything up?

If your capable of completing the LSX swap then you should be capable of either making custom tranny mounts, or welding in the sheet metal tranny mounts out of a manual FC.

I am amature fabricator at best and I did the latter acomplished in 1 weekend in the driveway of the townhouse where I used to live.

you also need a clutch pedal and master/slave etc.... shouldbe that hard with swapping everything else.