i would tear it all out and build fresh the way you want, it looks like your drawing would work out good
great part about scratch is you get to do it the way you would like it not the way that somone else did just because it was quick and easy.
Ten4. Was curious what others opinions were on it. Wasn't to sure bout the empty space under the rear boxes. Boat doesn't seem to drain that well with this configuration, the drains are underneath each rear box but water got trapped in between the stringers against the transom do to the flow through holes of the stringer against the transom becoming plugged. beleive this issue was the major reason to the rot, water trapped and it just sweated underneath the deck rather than drying out.
