Bernie is the expert on this,he infact got angry about people cutting the carpet badly around the shifter as their was no need for it!
as long as the shifter is bolted down tight enough and the shift plate is above the carpet, i.e shifter,shift plate,carpet,tunnel order it should work fine.
I always put the car in second before removing the shifter, then bolt it in in the second gear postition, i've found this method the best for the least adjustments.