Personally, I never go to Santa Cruz without stopping at 2 particular food places. Saturn Cafe, which is a vegetarian restaurant. I'm not vegetarian, myself, but they have an FLT (fakin' bacon, lettuce and tomato) that's fantastic. I also make sure to have the soup, as it's always good, regardless of flavor. The second stop is Marianne's Ice Cream. You won't find better ice cream anywhere. Try the Alice B Toklas Fudge Brownie flavor. The best!
There's a crepe place that I quite enjoyed for a late breakfast one time, but I can't recall the name of it.
Can't help with clam chowder as I despise seafood.
And I'm completely jealous that you're going to Santa Cruz! Been trying to figure out how to afford a trip up there this summer. It's my favorite place in the world.