So the gaps were pretty big to fill with epoxy in their entirety, so instead, I first added a few shims made from slivers cut from an old credit card, and epoxied that stuff in place. Now with the top cap secured, I had the choice of using putty to fill the gaps, but instead I opted for a different technique. One of the methods of gluing resin parts or filling small holes is to put a little liquid resin on the joint or in the hole and hit it with a blue laser to cure it. The curing is nearly instant. A few passes with the laser and it's solid.
So for filler I used wadded up paper towel pieces, wedged in the gaps and shaped to fit the area, then soaked it with resin and hit it with the laser. If done right, it will flow and blend in and look like it's a continuous piece. Here is a photo showing an area which i filled in, because I wanted to not only blend it in, but since the top piece is a reprint of the top 3/8" of area below, I wanted to hide the "repetitiveness" of the texture. While you can still see the pattern repeat in places if you look close, it's not that visible at a glance.
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