Doubt it was a Sturgeon. I've done that twice and both times they were very lazy. Probably knowing they could do anything they want at any time. Probably a fouled King, but a Musky is a possibility or a big cat.
When you are getting to that size range 28' and above, the stability of a straight inboard and ease of maintenance wins out.
I/O"s aren't even in the conversation.
Same situation for me while Island camping in the St. Lawrence. Tow Boat told me 3-4 hrs. I drifted to shore and tied up to a tree, next to a private launch. The owner allowed me the time to walk 3 mi to my truck and come back and use his launch. I did all this in under 3 hrs. Never renewed with TowBoat.
Not sure what you mean by locations near Rochester. I think it gets you perks at West Marine but the Roch store is pretty useless IMO. Better off investing in a reliable kicker!
You can switch the Perko from 1 to 2 or to both, while running without issue. The problem is if you accidently switch to off while doing so. That could be a real bad day!
Is the control wireless? I have heard the wireless Trollmaster's do the same thing. If it's not wireless, try isolating the wires from other electrical harnesses. Maybe run it through some flex conduit?