Hold off taking the stringers out until you have posted a few more pics. Ordinarily, the aluminum stringers are left in. Why do you feel the need to remove them?
I took another look at the photograph you posted here - when I saw this the first time, I thought that I was looking at a pinpoint hole in the side of the boat itself. Now I'm not so sure. When I saw it the second time, I had the impression that someone had cut a rectangular piece of aluminum out of the hull, which can't be right. Which part of the boat is being depicted here, and can you post a pic from further out? Is this a piece of the boat below or above the waterline?
As for transom removal, you need to remove the motor, if that hasn't been done, and remove all mechanical components attached to the area. You need to remove every rivet/screw that is holding it in, and you need to grind down the heads of the drain plugs from the splashwell and punch them out. There's a pic of this at post 14 in my 16' Naden thread below. You'll need to remove the splashwell cap (the strip of aluminum running along the splashwell). You'll need to remove the cornercaps on the rear corners, and bend up the aluminum on either end. There's a pic of this in progress on jasoutside's 22' Islander resto.
I found the video below from jeepcollector quite useful (I think he's on here somewhere).