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I recently rescued some metal GW minis from eBay and decided to strip them. I started stripping them in Simple Green and noticed large portions were covered in super glue. After transferring the minis to a jar of acetone to remove the glue, I've noticed the minis are now very dirty looking. Some patches of the mini are still white and shiny, but others are matte and grey.

What's caused this? How do I fix it? Will this affect the quality of my paintjob?

Can't really tell without pictures, a couple of phone snaps should suffice.

While I'm no scientist, I do have experience with what you're talking about.
Some people say that it's primer "staining" the metal after it's been on too long, others that it's a tiny layer of oxidation on the metal. Either way to answer the most pressing question, it will not affect your paintjob. After I scrub my old metal minis I just reprime them and they're good to go so don't worry!

I would suggest soaking your minis in brake fluid overnight and then scrubbing them with a toothbrush and some dawn dishsoap. after you remove that try brushing them with some aluminum polish and watch them shine like brand new!

Honestly, that minor discoloration you've got after stripping the paint off isn't going to affect your paintjob. Prime over it and you'll never even notice it.

Oxidation/discoloration/stains are not a big problem towards painting the model.
Nevertheless, after stripping (via acetone or other solvents) - or after unpacking new metal minis- I generally wash metal models with dish soap or toothpaste, rinse, dry...
Then I suggest a brass brush in a rotary tool (dremel or otherwise): don a suitable mask and glasses for protection, then brush the whole model with care for the model (and your fingers!). The model will be polished without losing detail, but this helps cleaning mould lines, too. After polishing and priming, paint applies more smoothly.

THF or ethyl acetate do wonders on metal, though I lately stripped a totally horrible Kharn from his disgrace and the mini remained stained afterwards.