Willy,

The main thing you're looking for is a smooth even coat of epoxy where the weave is filled. What you should be doing is keeping the sander level to sand down the hills. You stop standing just before the level surface gets into the glass (or wood if the panel is unglassed). If this leaves you with a uniformly sanded surface, congratulations! You're done!

What's more likely is what you're reporting - a scattering of shiny lakes over a dull continent. You can't just sand those away because you'll be following the depressions and end up with a sanded bumpy surface. Instead, you need to paint on another coat of epoxy, but only over the shiny spots. That will fill them in and raise their levels to above the average while leaving the average level alone. Then, sand again concentrating on the newly-coated areas and see if the shiny spots have shrunk or disappeared. If not, add more epoxy and repeat.

Pinhole-sized or smaller shiny spots are OK, but anything larger should be filled and sanded.

You should definitely avoid sanding into the wood. It's obvious after the fact if you've hit wood, so you'll know. If you have an accident and go too deep, recoat the bare area with epoxy. The wood has to be potected.

Laszlo