Well a very fast chip at 64MHz may help.

But using another approach I guess it is possible with slower PIC also. You may use the CCP module to capture the rising and falling edge of the pulses in regard with the Timer so the PIC will capture the timer readings. Either just waiting or doing other stuff while the ISR will just transfer the timer value to your variable.

With 1200 readings you will have to count double that. Rising and falling edge so is 2400 reading and I guess double that also, for the quadrature readings. Finally your pulse to pulse time may be about 200usec. Not too demanding but fast.

Ioannis