Hi Joe, with the cap still on the boat it'll be hard to get consistent measurements to the top of the stringers. It might take popping the cap loose and sliding a 2x4 under it and across the hull to get real measurements. I found out that my starboard stringer was 3/8" lower at the aft of the hull as the port stringer. I lammed more glass (6 layers of 1708) along the top of the stringer to correct that problem.Are you talking about the liner over the hull sides that you see in the last picture - the liner that covers the hullsides? As I mentioned earlier, I'd gently pop them loose and take them out of the hull, you'll be able to re-use them later, to save you fill/fair time. This way when you lay the floor in, you're measuring and tabbing to the hullsides, not a liner.So, pop the liner and remove from boat, unscrew the cap and pop it free, use a 2x4 to slide along the hullside top and get good measurements and repair what you need to. Then move on to the next step in your plan. My $.02