By definition, an '01 Mustang motor is a PI motor but it wouldn't hurt to verify. The heads should have 'PI' stamped on the ends of them (should be able to see it stamped on the back of the heads if the motor is out of the car). Other external clue: PI motors only have one temp sensor and it's on the passenger side of the coolant crossover on the front of the intake, where NPI have a 2nd sensor near the thermostat housing; The intake runner closest to the front of the motor goes to the driver's side of the motor on a PI intake and goes to the passenger side on a NPI intake. There's probably a few other clues I'm forgetting but beyond that, you'll have to check casting numbers.
I'd be concerned about a damaged cam support. That head may need replacement. The cams run directly in the heads - there are no bearings - and the caps are matched to the towers so even if you just replace a cap, you may have trouble in the future since they are supposed to be machined together at the factory.
A 2000 Mark VIII motor? 1998 was the last year for the Mark VIII. May want to double check that. Mark VIII swaps are popular though. Put a Cobra intake and exhaust on it and you've pretty much got a Cobra motor. Another popular swap is to take a MKVIII short block and put 2V heads on it for a big boost in compression (flat top pistons on the MKVIII) and a big savings in weight with the aluminum block without all the hassle of a 4V swap.
Ah, thanks for clarifying that. I knew there was a difference in the intake/induction but couldn't remember the exact details. It must've been the 5.0s that had the low profile intakes.