BT,
When they pulled the bottom did they also remove all the gears to look underneath them? It appears they would realign easy enough. (Excellent pix of the bottom by the way)
And I hope they changed the countershaft seal too since it has been opened and exposed.
Staying tuned for the next installment of the manly soap, "As the crank turns."

A word to the wise is not necessary. It is the stupid ones who need the advice. Pat