One small question is --- what did you mean by "have my doubts that the OP will have success wandering off the standard path and into Timer/Counter country with register settings" ?
No worries for you.
The OP was a self proclaimed newbie who was "not well acquainted with Arduino yet". He even appeared to be short of pins on a Mega somehow and couldn't figure out how to change anything around to free different pins.
Using the external clock source as a high speed rpm counter is very much recommended when interrupts techniques start to fail.