Any idea what might be used to cover the tour pak lid holes that looks decent and would be waterproof or at least water resistant?
You could have a couple small plates engraved with anything you wanted and place them over the holes with double sided tape. Anything will work that is uniform and looks like it is there on purpose and not as a cover.
I bought a secondhand tourpak and removed some of the things mounted on it. I filled the holes with araldite and let it set before repainting. Covering with reflectors is a great idea, but I suggest you fill the holes first.