thats the problem with body work...you never know if your doing it right...i ran into the same problems when changing my floor pans...I will give you one short advice...if you go in, go all in or your just going to chase your tail...I was about 90% done with my floors then decided to sand blast my engine bay and found tons more rust...if i was to do it over i would have just driven it since it was mechanically sound and found a better starting point. But dont give up, just make sure you know what your getting into before doing the repairs.