I've done some similar work on a Gottlieb Hit N Run... I learned a ton from Todd Newman... here's an exerpt from a few emails and links that show our work... even though there are differences in what you're tackling, I'm sure there's something you can take away from similar work...

I would get the wood that way you want it:
Strip, dig out the dirt and crap, bleach (oxalic acid), tint (lacquer
and mixol), spot clear with an 2 part autoclear (brushed on would be
ok), sand flat, then make your circles. At least that is what I did.
You could also use clear epoxy, i've done that.

<picasaweb links removed - no longer active>

--- More info on Hit N Run Don Owen ---

Talk about one of the biggest pains ever in pinball restoration...
nasty pop bumper areas that have been chewed up over time, and left
marred and battered. Thanks to Todd Newman, I was able to get these
areas in much better shape - I used most of his photos and advise over
the many hours of restoration work. Although not perfect by any
means, not bad for my first attempt at pop bumper repair, as well as
creating the circles and painting with an airbrush. Circles for the
pops were created out of frisket film, cut by compass modified with an
exacto blade explained so well by Todd; this method worked great, and
would recommend it to anyone who demands a better looking and
permanent way to fix these areas. See pix of before and after here:

https://photos.google.com/album/AF1QipNzrr_cFv_Kv5Ixe_cFvwAhawHA_QtusAu8FCnc