Shakemsam

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!

Frying the alternator for starters.

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!

Distance apart might but up and down should not. Biggest issue would be if they are the same frequency or cone angle. My2cents

Unfortunately, you will most likely have to remove the runner as well.

I always ran on 1 and occasionally would run on 2 to keep everything charged. I always tried not to switch while the main engine was running.

It's not over thinking! The more connections, the better chance of a bad connection! In a perfect world, your Battery should go to a battery selector switch, Switch common to main engine as well a separate feed to a breaker continuing to a fuse panel, all capable of handling the amperage load. Your kicker directly to the cranking battery, but ideally to it's own. Bilge float directly to battery with an inline fuse. FWIW...I run a breaker and panel feeding my console electronics and another breaker and panel for the stern (riggers, 12v supply, Depth Raider, TrollMaster, Remember, that 6 amp alternator won't put out 6 amps at idle and most likely not at trolling speed.