Is it possible that I fried an MCU pin by performing a continuity test
Both scenarios (damage from using a multimeter or damage of a particular pin from soldering temperature) are very unlikely. 

My guess is that you either have a firmware problem (some sharing of peripherals that have to be disabled) or you have damaged them in some other way such as too much voltage from ESD or an ungrounded soldering iron tip. 

Since you have a board that is working (presumably? with the same firmware), it would have to be something that is undefined during startup to be a firmware problem.