Dustin,
That boat looks like a fun project.
Either the 36 or 30 pound trolling motor should work fine for
that boat. If all things were equal I would go ahead and get
the 36# one and just run it at the low speed, then you have
the extra power if you ever need it. As far as the shaft
length just measure to make sure your not hanging too low
below the boat for when you get up real shallow.
Any good deep cycle battery should be OK. I got a marine deep
cycle from Costco and I can run my 14' v-hull all day long on
it.

Good luck!