When Kev fitted my CA the only part of the trans tunnel he needed to modify was the top of the tunnel where the new shifter went. This was cut away and a piece of thin sheet metal was welded in to allow room around where the new shiffter went and to cover up the old shifter hole. There were no firewall mods at all.

It really depends on how showy your car is going to be. If it's going to be a show car with a detailed undercarriage then doing it pre painting would be wise but if it's an everyday car the carpet is going to cover the mod anyway.
Matty