That store was The Record Exchange (subsequently renamed The Sound Exchange). They closed their doors a few years ago, and recently a fast-food Mexican restaurant called Baja Fresh set up shop in that space. Interestly enough in these days of big corporate tyranny, the Baja Fresh owners succumbed to local pressure and not only decided not to paint over that mural, but actually delayed their opening by over a month to incorporate some of Daniel Johnston's "look and feel" into their restaurant. (To tell you the truth, I don't recall noticing any of his artwork the one time I ate there, but that doesn't mean it's not there.)
Daniel has a big supporter in local bassist/producer Brian Beattie (Glass Eye, etc.) and his ex-bandmate Kathy McCarty (misspellings unintentional). I've seen Brian post on TapeOp, so you might track him down there. (He might post here, too.) Other notables who have covered his work include The Reivers and fIREHOSE (or was it the Minutemen?)