The stringers were fabbed out of the boat and set in all at one time like a liner. There should also be a liner covering the inside hullsides to the cap. If you can get that off gently, you can cut down the lower portion by the amount you raise the deck and re-use it to cover the unfinished hullsides.
You'll need the aft 18” or so out of the way when you rebuild your transom, so it only makes sense to do the transom first. Then that will give you one last chance to check the hull for square and true before you immortalize it by rebuilding the stringers.
X2 with mshugg. Also lay a board across the cap and get good measurements to the top of the existing stringers and document them. Document the existing stringer system as far as distance from each other, from the hullside, height from hull bottom, width at top and bottom. This is history of the original hull in case you change your design mind, like raising the deck height, which is pretty normal..You will be changing the low point in the hull when you rebuild the transom (maybe it has already been changed if rebuilt before). Here is a link to where I explain the thought compensating for this with the addition of a PVC pipehttp://classicaquasport.com/smf/index.php?topic=13148.msg133124#msg133124Here is a link to where I show what is actual problemhttp://classicaquasport.com/smf/index.php?topic=13148.msg133556#msg133556Here is a link to Hawgleg's rebuild that shows the PVC pipe installation to keep a drain at the new low point of the boathttp://classicaquasport.com/smf/index.php?topic=13148.msg134262#msg134262