What's the frequency of incoming pulses to the "master counter" and "regular counters". Since you need so many counters they can't be high speed counters, so need to be constructed out of normal up/down counters. If your program size is not too big and you don't use complex custom functions, then the regular counters should be able to count at 50Hz or lower. Best is to test it with your actual program to know at what program length it started losing counts.
