I think your setup will definitely benefit from having a pre-pro and dedicated amp arrangement rather than an AVR. Further, there is no reason to limit the amp power based on the speaker rating. Since you will be calibrating, etc. having a more powerful amp will ensure that there is sufficient headroom for the speakers. That said, there is no point getting a 1000W/channel amp either since that would be overkill and a pointless expenditure.
If the M-501s have sufficient power for the fronts and work fine, there is no reason to get rid of them. I suggest moving them to power the four surrounds and adding a different dedicated amp for the fronts.
Integra DTC-9.8 makes for an excellent pre-pro, reviewed
here. I believe the street price for it is about $1200.
For the frontstage amplification, do you have a preference for amp technology? Class A, Class AB, Class T, etc.?