They run the plate, it was for a Jag, not a grey honda civic hatchback that the guy saw. So much for that. They can't run similar plates... they have to have an exact match.

Bull. They can do similar plates. I know because I do this all the time. Of course if they wanted to is another matter alltogether.
The way I'd do it is search for a list of all the honda civic hatchback's that are in the San Francisco area and then cross reference that result with the number plate I got from the withness. This has worked for me many times.
Sounds more to me like they weren't in the mood to do their job right.

I turned down the fingerprinting, no point... everything was smudged

A shame. You'd be surprised how much fingerprints you can get out of a car, and also in areas you wouldn't expect them to be. It's not because you can't see the prints that they're not there.
Of course that's a moot point now since you've already used the car since the break-in and most probably contaminated the evidence by now.

Again, I'm very sorry for your loss. If you think there's anything I can help you with, don't hesitate to ask.