1. What hardware did you use to connect the 2x2's? Screws / nails ect.
I used deck screws to attach wood to wood, in a few places I used strongties.
2. How did you connect the trolling motor platform to the boat/framing?
The previous owner had drilled holes through the gunnel, I reused these holes and mounted the platform with stainless bolts with nylon lock nuts. Two of these bolts run through the trolling motor mount.
3. What hardware was used for the seat bases?
I used stainless screws, they run through the base, plywood, 2x4, and in to the aluminum seat. I was a little concerned how this would work out and would rather have used a bolt, but the have proven to be sturdy so far. Each seat base has 2x4's under it.
4. Are the seat bases on top of the plywood or flush with it?
They are on top, but once they were secured with the carpet in place they sit pretty flush. I used a hole saw and cut the hole through the plywood a bit bigger than needed.
I then carpeted the plywood, after the glued dried I cut an X in the carpet where the hole was and folded the carpet through the hole then glued and stapled it to the backside.