It looks to me like those places with coloration still have a little sealer left on there. I had a similar problem with a refin I did a few weeks ago, the sealer was laid on so thick that it took a good while to sand it off. You could still definitely try chemicals though.
As far as the grain matching goes, I personally don't think it is that great, but not terrible. You could clear it if you want, but I personally would probably do an opaque finish. I just did on a solid maple guitar that I have been refinishing. I love the look of maple, but the grain matching was an abomination, so I painted it. Just my opinion, however.