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This is an example of cutting the gunwhales to remove the rear cap to get to the transom Filling the seams on the go back is Easy and won't be noticeable.
The motor is off finally and I am trying to figure out a way to cradle the boat, it is a roller trailer. I am only taking off the splash wells to do the transom. I attached some photos I was playing with 2x6's to get some ideas. I was thinking of doing one stringer at a time. Also I took most of the plywood out before I knew about a cradle and these stringers are completely rotted how do I know if the hull is already twisted?
If the hull is possibly distorted, I suspect you're going to have to take measurements of the fore and aft spans, from gunwale to gunwale, and possibly a diagonal or two. May benefit from seeing if anyone with the same make/model can help out in what you should be seeing, as it's not likely to find manufacturer specs with that level of detail.
If you've got a rollers instead of bunks, you definitely want a cradle.
Trailers can flex, weather bunk or roller. I laid a 2x6 on a concrete floor, put the boat on it, completely on the keel. Measured/adjusted till it was completely level and made fixtures to keep it straight. Before each glass layup, measured to make sure it haven't moved, and continued work.