Very odd process but somehow it worked! lol. Thank you for all of your work and help! This is an awesome ROM and it is not even fully complete!!!
Ok, that confirmed my suspicion and I just tested and was able to reproduce your issue.
It seems that if you do a "format system" in CWM, it seems to format system into a format that is causing the bootloops.
You should NOT be manually doing a format system in CWM before flashing any future CM9 updates since flashing the ROM will automatically format system into EXT4 format properly.
Doing a factory wipe/reset data is fine.