Apologies, but im not sure what you mean by "instrumenting" the interrupt code?
Add some code to keep track of which interrupts have actually occurred, say by putting in:
uint32_t isr = PIOC->PIO_ISR;
PORTC_INTERRUPTS |= isr; // keep track of all the PORTC interrupts that have ever happened
And then some other code to LOOK at the PORTC_INTERRUPTS globals.
The clz-based code really shouldn't be any more jittery than the old code, especially if only one pin is interrupting.
(and I've now looked at the code - it LOOKS like it only enables interrupts on pins that you've actually called attachInterrupt() for.)