With the motor tilted up, have you tried to pull down on the skeg and see if the transom flexes. If so, you will need to redo that transom, if not then you can wait and do it later.
Second question: the foam in the stringers...is it serving any purpose? Could one pull the transom, devise some sort of plumbing snake styled tool and root out the [wet] foam and then glass the transom up and be done with it? I'd already have drain plugs installed in my stringers so that if the now hollow stringers took on water from a source other than my transom, I'd know it and have a way to evacuate it...
Would I be selling myself short to just do the transom and not go ahead and tear it all the way apart? I guess my concern is that I'll be duplicating work if I do the transom now/soon and then 2 years from now decide to tear it down to nothing and build it back...is that a valid concern?