Nice to be back on a project and keeping it in the family, but I have to ask, is that all pressure treated plywood?
It looks dry, but is it kiln dried? And did you seal it in anyway before installation?
If it's not high end marine pressure treated plywood (like what pontoon boat makers are using) the chemicals in it can be caustic to the aluminum of your boat.
Hit the exposed transom plywood with some paint or spar varnish. It's showing it's age:
When you get a chance, it'd be well worth pulling the 'newish' transom ply and selling both sides, all the edges and through holes really well.
Depending on where you boat, the missing splashwell pan might be a good piece to put back on if you still have it. Even if you boat smaller, calm waters, slowing down off plane, the following swell can wash over a short transom.
Not many StarTreks in the Starmada, check out the
Starcraft forum, lots of good stuff in there for tin boats