I have the K-code manifolds with no clearance problems, but it's a Ron Morris unit that loops around in front of the fuel pump, then back along the oil pan rail. The Mustang Steve setup with the fox cable or the Modern Driveline one loops much farther back and may have interference issues with the #5 or 6 cylinder exhaust manifold or header tubes. IDK. Some headers won't work at all with the T5 bell and any cable clutch because they tuck in too much and want to occupy the same space as where the clutch cable goes through the hole in the bellhousing as it heads back to the clutch fork and access plate.
My car is a 66 with a roller 5.0L with Edelbrock heads, torker 289 intake, dual exhaust and has been lowered 1/2" from stock. It still has the stock style fuel pump, A/C and manual steering.
Daniel