If the goal is to shop by color/style, I would filter out the cars that aren't available in the selected color. Showing the little gray boxes provides no benefit at all. I would also eliminate the pagination on the listings. Pagination almost always detracts from the usability of a site. In your case, it makes it much harder to compare vehicles within the search results. And, when you remove the pointless grayed-out boxes, the page will never be that long.

I originally filtered out the vehicles not available in the color, but it was confusing when vehicles popped in and out depending on color. If my vehicle isn't available in red, I want to know that.

As far as pagination goes, I'm with you. I'm still on the fence about whether or not to ditch it.

Perhaps group results by availability then?

Like:

   Available vehicles A-Z
  ------------------------
  Unavailable vehicles A-Z

Why not ditch pagination? What is it adding to the site?

More confusing UI, IMO.

I'll probably kill pagination, though.