So it turns out kyuusaku is The Man! I swapped out my 100M osc for a 25M osc and my NES clocking is now much more accurate!!
With 100M the best I could get was:
DCM Output = 44MHz
2A03 = 44M / 24 = 1.83 MHz (~2.23% faster than original NES)
2C02 = 44M / 8 = 5.50 MHz (~2.23% faster than original NES)
With 25M I've got:
DCM Output = 21.4286 MHz
2A03 = 21.4286M / 12 = 1.786 MHz (~0.227% slower)
2C02 = 21.4286M / 4 = 5.357 MHz (~0.227% slower)
As you can see the 25M option is MUCH better!! Nice little upgrade!
I am still sacrificing the clock feedback correction loop but it doesn't seem to matter from what I can tell so far - this is certainly only because I am clocking at such low rates though. I will need to check the timing analyzer output but I've been playing my NES for a while now with a bunch of different games at this new frequency and it seems fine. If there were any major timing issues I probably would have seen it by now.
I'm not even sure that I will bother getting the 14.318M osc cause the 25M option is already so close. If I purchased a 14.318M osc I could get the following:
DCM Output = 21.477 MHz
2A03 = 21.477M / 12 = 1.789 MHz (~0.001% slower)
2C02 = 21.477M / 4 = 5.369 MHz (~0.001% slower)
Anyway, thanks again for the help kyuusaku!
Jonathon