I did this swap last weekend and left my long-runner manifold in place. Only really tough part was getting the clamp that holds the hotside to the center-section back on. I actually couldn't get it myself but ANNA did! Unreal.
Anyways, you don't HAVE to take the manifold off but if you are short on hands it might save you some grief.
Also, If you've been having problems you might have fiddled with your boost control to try and compensate....turn DOWN any MBC you have as I hit 39.5psi on my first 4th gear pull on the new setup
EF4 = do work!