Just cause parts are new does not mean their good.
"I'd pull the bowl (still installed) and make sure fuel IS flowing out of it." Did you do this??
Make sure the coil is installed correctly-They often have stamped in them "up".
Check spark (with the new parts) and rule it good or not.
Coil failure will OFTEN work, then loose spark after getting warm/hot.
An air filter will not shut down an engine after a certain amount of run time,
UN-less the loss of air flow fouls the spark plug.
Valve clearance / adjustment is easy. With the intake valve open, check the exhaust clearance.
Likewise, with the exhaust valve open, check the intake. I doubt this is the issue but should be checked