The Tohatsu regulator/rectifier will work just fine without being connected to a battery, so it should not have failed.
As for powering a blower, keep in mind that the charge profile does not make very much power, except at WOT. I have a similar setup in my HR-28, except with the 6-amp 9.8. Of course, my boat does have a house battery. Yes, I can run the lazarette blower with the help of the alternator, but at slower speeds, the blower draws more power than the alternator makes.
I would suggest that at higher speeds, the exhaust will be behind the boat anyway; it's at slow speeds and reverse (when the alternator does not make much power) that you want more fresh air.
See if you can setup the lazarette compartment to get fresh air passively; either by opening the hatch, or with clamshell or similar vents.