Yes, the bridge needs to be moved back before the saddles could be moved forwards to cover the racetrack holes and your understanding of bridge positioning is correct.

You could got a faulty string where its been over-stretched in one small area so you've got a much thinner section, which would throw the normal intonation out.

I'd have thought it would be a poly finish. Very unlikely to be nitro lacquer unless it was a US-made Peavey custom shop guitar.

I recently mended an Ibanez acoustic that had a side-mounted jack socket that had been ripped out when the guitar was dropped with a jack plugged in. I mended the hole with a mixture of wood and resin, then sprayed the repair area with black auto paint and clear auto acrylic lacquer. After sanding and polishing, it was just about invisible. I fitted an end-pin jack instead - much stronger!