Acids neutralize uncured epoxy, which is why you can use vinegar to clean up spills. It's also why epoxy doesn't work well on oak, which contains a lot of tannic acid. If any citric acid residue from citrus cleaner was left in the wood, it would cause curing problems when the new epoxy/glass is applied. For that matter, I would also be leery of using vinegar on bare wood.

Neither of these should be a problem if the wood was seal coated before glassing, as long as the area is washed carefully to remove any acid residue.