I may be too late for the OP, but my 2 cents...
+1^5 for Alembic,
Given their quality and multiple locations in SF, I wouldn't recommend Cha Cha Cha and Squat & Gobble. I haven't gotten anything noteworthy at Ploy II-- what's good there?
One good spot in that vicinity is Parada 22. The food is fresh, and despite their non-use of lard, their mofungo is better than at least the touristy places in San Juan. It's not the best or most traditional PR food in the world, but since it's only one of two PR places in SF, it's my highest priority place there next to Alembic.
Citrus Club is a decent neighborhood fusion noodle place. Their sauced edamame appetizer is a good starter.
It's a few blocks of walking, yet closer than Magnolia, but Haight Street Market has really good sandwiches. I've always been happy with their cheese and produce selections, and their prices are better than that of Whole Foods.
Head up to Ice Cream Bar for a shake. Or a sundae. They had a guiness milkshake and another special for St. Patrick's day. Don't know if it'll last, but it's nice to see specials there.
Stanza for espresso.
Magnolia is the best brunch spot in the area--- Zazie and Pork Store Cafe have extremely long waits, so they get nixed from the running.
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