What did the old clutch and flywheel look like? Why are they being replaced again: power upgrade or problems? As in is this a new problem or an old problem that's ruining clutches?
Do you have or can you rent a magnetic dial indicator? I would put it on just on the outside of friction band of the flywheel and spin the engine over slowly by hand. With the bolt hole problems maybe the flywheel didn't get on the crankshaft straight. Same with the input shaft of the trans: make sure it isn't bent.
Do you want to pull the trans after a resurfaced flywheel comes back to haunt you with those "cementite" hot spots? IMO it's ruined garbage.

Just unreal that the hot spot is only in one area. (It's possible Kevlar just leaves a black mark without cementite temperatures, but, it's still a big problem. Good question to be asked.)
Cementite is iron carbide formed by excessive heat and will be thicker in the area. So the formation of cementite expands to becomes a high spot and the high spot gets hotter and forms more and deeper cementite. If the flywheel grinding misses any of it ... it comes back quick and is nothing but trouble. Note: Common for the undersized brake systems, due to CAFE, to get hot spots like this that turning doesn't fix. The "carbide" turning tool, yeah same material, bounces off cementite and leaves them alone as high spots thus why grinding is the only hope. Myself I simply toss brake rotors and flywheels because it's too much of an expense or PIA to mess with it again in 3000 miles when cementite comes back.