what about adding something to the FAQ outlining the fact Emplode takes ages to rebuild the db with no discernable progress activity during the initial stages?

It doesn't, normally. The problem was in the "checking media" stage, not the database rebuild. Two separate issues, usually unrelated, coincidentally happening at the same time for you in this instance.

I'd rather see Emplode give better feedback about the checking media stage. Perhaps warning you that this particular one is gonna take a long time. Or maybe even simply change the name of the stage to "checking media (may take a long time)".