Yes i have access to the interior of the plug and yes i planned to glass it in as well. I filled the exterior with 3 layers of glass to build it up flush and will do the similar to the interior patch. Thanks for the pointers.Great work Semper. Are you able to access and dish the interior side of the holes in the transom? Ideally you want some layers of glass on both the exterior and interior faces that will bond to the surrounding transom and lock in the "plug" - unless you're planning to fill the full thickness with mat or cloth. You don't want a point impact on the holes to crack or dislodge the plugs.
Re: joining stringer extensions, IMO you're fine since the engine beds span the joints (hopefully at least 2 bolts on each side?), but just for your and others consideration...
The stringer and extension need to act structurally as one piece, whether it's to anchor the engine, to reinforce the hull, or both. The decision about joint type depends on its original construction. If the glass covering is relatively thin (say, <1/8") then the core - in this case wood - is the structural member and the glass is only for tabbing to the hull, moisture and abrasion resistance. If the glass covering is thicker (say, >1/8") then the core is more likely a form and the glass, a hollow tube, is the structural member.
So as you would imagine, if the wood is doing the work, you'd want that joint to be a strong one, and use a scarf joint like Xbskt suggested. (or in your case, reinforced w/ engine beds)
If the core is just to form the glass, then the joint doesn't matter.
I think I've heard Tony A, "float" the beds like you mention. The beds may have a tendency to fall off "plane" when attaching to the stringers if they aren't perfectly flat or plumb. Anyway, that is how I took the information that I read. So, he would use a jig to keep the plane of the engine beds fill (bed) the small inconsistencies on the stringers to match the new aluminum beds. I don't think you need the adhesive qualities of epoxy for this. If you want to do it like this, maybe a H&D putty or some sort of pourable casting resin may work. IMO, it may be a bit over kill better suited to the perfectionist.When I float in these stringer brackets(the engine beds) what material should I be using? Thickened epoxy? I would probably need a few tubes. Is there a more cost efficient way?