[Arran]

Joseph;
The dye I'm speaking of penetrates the wood, it will take blond wood and make it any colour you like, I think it's aniline based like Rit fabric dye, and you can mix it with either alcohol or lacquer thinner the latter if you want to colour lacquer. I have some that my late uncle got from Lee Valley, but I'm sure you can get it elsewhere. I also have a bottle of Mohawk penetrating stain that I picked up from the bottle depot, but I haven't tried it on anything yet, but understand it's similar to the crystals you have to mix up.
I have used fabric dye to darken wood so I didn't have to use as much tone spray over it, but that was mixed into hot water, and I applied it hot onto the wood. None of these will get rid of the dark spots, though it may make them more brown rather then that barnboard grey, but they will obscure them enough that they are not as noticeable since the background colour will be closer to the spots. One advantage you have is that you have the cabinet shoulder you removed to experiment on as a test strip, so you can see what hides the spots best.
Regards
Arran