I would be concerned about using a petroleum based solvent on an asphalt shingle (which is basically petroleum based). Any possibility of painting the shingle a color that would match itself? It wouldn't be perfect, but I don't think cleaning would either.

Or, could you get some of the shingles that were not used and just glue them over the top of the painted shingles? Nobody would probably notice unless you pointed it out.

Shadygrove is right about not using a solvent on asphalt shingles.

I would however be a little concerned about shingles glued down that were not woven into the installed roof, might create a catchment that would hold water and cause problems. And the irregularity might be more obvious than you would like.

Replacing one or several shingles without compromising the integrity of a roof is not difficult. Google "shingle repair" and you will find any number of pages showing how it is done with everyday tools. I did this recently to cover a roof patch where I had removed a chimney, and there was nothing technically challenging about it at all. The trickiest part was not sliding off the 5/12 pitch roof.

Since your roof is new you should be able to buy matching new shingles, but if not just swap out the painted ones for some others from an inconspicuous part of the roof.

Thanks for the advice...I'll go outside this weekend and frown at the roof a little more....