Sorry, haven't been here for some time.
I dunno understand what exactly you want, so here just a short example of running Timer counter TC0
at 42 MHz. Maybe this is something that can fit your needs.
Sketch starts and reads (CV = counter value) counter.
void setup(){ Serial.begin(9600); }
void loop()
{
unsigned long v[10];
int i;
PMC->PMC_PCER0 = 1<<27; // PMC: Enable Timer TC0
TC0->TC_CHANNEL[0].TC_CMR = 0; // Control mode reg.: set Clock to MCK/2 = 42 MHz
TC0->TC_CHANNEL[0].TC_CCR = 4 + 1; // activate Timer: // Start + Enable
Serial.println("---------------------------------------------------------");
Serial.println("------- delay is not exackt, TC0 is! ---------");
Serial.println("---------------------------------------------------------");
Serial.println("Delayed Readout (24 us -> ~1000 Ticks)");
TC0->TC_BCR = 1; // restart(sync)
for(i=0; i<10; i++) { v[i]= TC0->TC_CHANNEL[0].TC_CV; delayMicroseconds(24); }
for(i=0; i<10; i++) { Serial.print(i); Serial.print(": "); Serial.println(v[i]); }
delay(5000);
Serial.println("---------------------------------------------------------");
Serial.println("Endless Readout (1s -> +42 000 000)");
TC0->TC_BCR = 1; // restart(sync)
while(1==1) { Serial.println(TC0->TC_CHANNEL[0].TC_CV); delay(1000); }
}