There are probably a couple of issues here. The Edelbrock Performer RPM sits about 1.25" higher than the Pontiac intake manifold. I can't say if the factory air cleaner base will clear the linkage of an Edelbrock carb. If you have the original Pontiac intake, quadrajet carb, air cleaner and shaker from the Trans AM that would be the easiest and cheapest way to go.
My understanding is the Pontiac Intake manifold is pretty good. The Performer RPM is lighter, horsepower gains might be minimal. I am running a Performer RPM with a FAST EFI system and had to purchase a EP-401 drop base air filter in order to have my shaker site at the correct height. My FAST throttle body didn't have any clearance issues using the EP-401. It is my understanding the FAST throttle body has the same height as a quadrajet.
If you don't want to go back to original intake and carb, buy a EP-401, see if it clears your Edelbrock carb. If it does fine, if not be prepared to put on a quadrajet along with the EP-401 to have the correct shaker height.
One other option would be to buy an Edelbrock Performer intake, it is suposed to be the same height as the factory intake manifold. It's lighter than the Pontiac cast iron manifold, but no performance gain over the factory intake.
Here is a link to my engine transplant, scroll half way down on page 2 to read my post on dealing with the shaker height.
http://www.transamcountry.com/community/index.php?topic=83455.40