I rarely do repairs like this, but have done some. You've done what I do for the most part. I would have set up a router with a template (cut on the cnc) and cut all the way through the p-tex. This involves some tricky adjustments, but with a dial indicator you can usually make incremental depth adjustments of about .005in until you are through the base. I then use our cnc to cut multiple patches each .005in bigger than the next. When I find the one that fits the best, I use it. The patches I've done have been much bigger. As long as 40in. I put the board back in a press rather than clamp. It then gets a base grind.
If the metal is directly under the base, it does present a problem. If you lightly sand the aluminum minutes before applying your e-poxy, you should get a good bond. aluminum will oxidize. This is what prevents adhesion to it. By sanding immediately before applying your epoxy, you should get an extremely good bond.