I've got a 42" 55lbs Minn Kota Riptide. Best investment I've made. I would definitely go with a 42" shaft, shorter than that and a couple fatties up front will have your prop out of the water.

Origianally got it because I got tired of watching my buddy fish while I sat on the oars. But it also works great for trolling. I recently switched from an Endura to a Riptide so I could fish the sound and tide water. (the 55 lbs is adequate in the sound if you stay close to the launch and watch the tides and wind, otherwise it could be a long trip back to the launch).

When trolling I'll bring up to 3 batteries, for a day of side drifting one battery is sufficient. You'll want to rig a longer battery cable to put the batteries up front, so the boat is balanced better. An easy way to do this is get some quick connects and a 6ga jumper cable. Cut the clamps off one end add the quick connects and you're set.