This is an little bit of an old thread, but if you are still considering this, my 2 cents is... All the people saying this will never work have obviously never used a system like this. While much smaller, my last boat was a 28' overall aluminum fishing boat that had a 15hp trolling motor that we used extensively for fishing. We used that motor in all kinds of horrible conditions, and never even got close to having the throttle pinned. Our biggest problem was that we would fish for hours, and the alternator didn't put out enough amps at low rpm's to feed all our electronics, autopilot, etc. We used it to backtroll into huge waves 40 miles offshore at Westport WA while halibut fishing and had multiple waves completely submerge the motor in green water. It never so much a hiccuped. I used it once in reverse, to pull us off a lee shore beach (We were on the gravel with large white caps pounding on us) in a horrible storm after we had fouled the main with a dock line in a disastrous boat ramp debacle.
I had an extra long shaft 15hp Honda, and it was mounted low. I used it many times in horrendous conditions, and it never once pulled out of the water or had cavitation issues. I think one of the first pleasure boat to cross the Atlantic way back when, had something like a 10hp gasoline engine. I would get a 15hp as they are similar price, and have better alternators, more power. The other aspect I liked, was that if you ever killed your batteries, you had an engine you could hand start, and with a little patience, charge your batteries enough to get the main started. The biggest problem you will have is figuring out Gasoline storage, and running it often enough so that when you go to use it, it isn't full of bad gas. Also it helps if the motor has a hose connection for flushing fresh water built into it, as the earmuff type flushers are a pain if the boat is in the water.