Sometimes there are problems that can only be fixed by starting from a "fresh" phone. It may be overly conservative (and time-killing), but if you want to be uber-careful -- and if you are having more serious issues, like boot-freeze and looped-flashing -- then do the following:
1) Flash latest OFFICIAL -shipped- (not stock)
2) Wait for phone to complete resets and installations
3) Flash radio of choice (or not)
4) Flash custom ROM of choice
5) Wait for phone to complete resets and installations
6) Clear storage (with or without formatting internal memory)
7) Wait for phone to complete resets and installations
Enjoy!