Floor and transom rebuild on '72 20SF

[tommy54]

I've been running my seacraft for a few years since I added aluminum plates on the transom to hold things together, and the floor really got bad this year so I tore it down the other day. It's a 1972 with the 4 stringer setup. Here's my plan.
Transom is being raised to take a 25" shaft motor, I like the balance of the boat so I'm not adding a bracket. This is a workboat and simple is good. I've been running the boat with a 369 pound Yamaha 90 four stroke, and I was happy with the performance. It hits 32 with a 15 pitch prop, pops up on plane quickly, and cruises at 26-27. The new motor is a 115. I plan to do the transom from the inside since I'm doing the floor anyway and I'd like to tie all of the stringers into the transom. It would be nice to get rid of the rear seats since they are never used, but I'm not sure where to run the rigging if I do.
I plan to raise the floor by an inch and a half or so. This boat runs lightly loaded nearly all of the time. It's usually one or two people and a toolbox on an inland lake.
A new fuel tank will go under the floor.
I'm up in the air about the liner. The storage and raised deck up front are nice for how I use the boat, but I can't see the forward half of the little keel stringer, and I only want to tear this boat apart once. The rear fish box thru hull drain has been filled and a new one drains into the the foam filled cavity between the starboard stringers. The hull to deck joint is in rough shape so I'm wondering if I'd be best off pulling the liner to build up the flange and recore the cap. Also, the front 6" of the boat (cap and hull)has a poor repair job from a pretty good collision. Any advice on whether to pull the liner to get access to everything or leave the little stringer alone and fix the cap from above?
I'll try to figure out my dropbox to get some pics up.
Thanks