Why not just leave it all alone and add thinner weather stripping out at the edges?

Here is a close upDSCF3529.JPG

Couple of points to ponder:
1. I use Liquitex. I've discussed this with their rep and he suggested I dump the tubes and use the bottles. I made this change 6-7 years ago and have not looked back.
2. I used to use the color matching wheel you have there. I dumped that in favor of this:
http://www.dickblick.com/products/magic-palette-artists-color-selector-and-mixing-guide/
3. #2 above will guide you to what colors to by. Do not go off the name, go off the pigment. Use pure pigments when possible.
4. In your description above, 2&3 are actually the same. Hidden features merely lack the back light to illuminate them.
5. For back lighting, I used this something similar to this - but an el cheapo from toy r us:
http://www.createandcraft.com/pp/artograph-lighttracer-light-box-10x12-inch-122271?istCompanyId=9d7dc72a-c353-46bf-b30a-94a77b390d40&istItemId=plpalwlrr&istBid=tztx&mobilebypass=1&gclid=CjwKEAjwocKtBRCf9d_Q5ovcyHASJAAHhJYOmaEnKGZJJ4zgHoQD4-J5wUChvWJjbQF5_dUEAQtoLRoCfabw_wcB
It was immensely helpful.
6. Unless you have a hair line to fix, translucent areas generally require scraping out, masking and spraying the whole thing. My results are here:
https://pinside.com/pinball/forum/topic/how-do-i-touch-up-backglass

Looking at my backglass last night, I'm in tough shape as well. I may consider popping for a re-pop or a bgresto.

Also, you might want to consider using this stuff:
http://ezscreenprint.com/

I've used it for "game over" features etc., with pretty good results.