I looked at the eq but dismissed doing it manually. Way to difficult! I tried running the YPAO with the eq set to "Front". It set the crossover to 120 in this case.
In regards to the frequency corrections the YPAO is doing I'm wondering if the receiver applies the crossover first then makes the corrections to the channel frequencies or does it make the frequency corrections overall to the overall sound of the speakers then applies the crossover freq based on speaker size. If it's the latter, then changing the crossover freq afterwards wouldn't have an effect.
