Hi Doovy,
For the shaft, what you need might vary and depend on where you decide to mount the bracket. And if you want to use the bar for steering, then you might want to figure out where you need to mount the motor and then obviously the bracket so that the steering bar will work. And that's assuming you'll be using that tie-bar system versus some other type of remote steering system.
Some of the things that come to mind that I would consider would be...
-the weight of the motor - you mentioned you have a 17' boat, so I would think about what adding 75-100 pounds on the transom would do to the dynamics of your boat, in terms of planing etc.
-ability to troll - some motors troll down better than others
-the power you'll need to troll into a stiff wind - yes bigger is better, but also typically heavier as well. Is that an important consideration?
-shaft length needed- maybe important, maybe not, still to be determined
-brand - what does the local dealer in your area carry? It's always easier to get parts from a local dealer if you break down.
-price - always a consideration
-is there an advantage to getting a motor with a generator to help charge the battery as it runs?
I looked up what Merc has available.
They have....
2.5, 3.5, 4, 5, 6, 8, 9.9 Horsepower models
-The 4 is a 4 stroke weighs 55 LBS and comes in 15" and 20" shaft lengths
-The 5 is a 4 stroke weighs 55 LBS and comes in 15" and 20" shaft lengths
-The 6 is a 4 stroke weighs 55 LBS and comes in 15" and 20" shaft lengths
-The 8 is a 4 stroke weighs 84 LBS and comes in 15" and 20" shaft lengths
-The regular 9.9 4 stroker weighs 84 LBS and comes in 15" and 20" shaft lengths, and there are also two other 9.9 models, the "Pro-Kicker" and "Bigfoot".
Now the 9.9 Pro-Kicker is actually designed for use as an auxillary trolling motor or "kicker" motor. It comes with a different gear set in the lower unit designed for trolling and also some other goodies, but it also weighs in at 108 LBS, in part because it comes with standard power trim. Will that be too much on your 17' boat? That's something you'll have to determine.
So there's some good info to digest, hope it helps.
I'm sure some of the other guys will have some good info and input as well.
-Chris