As far as bookstores, you're going to Powell's City of Books. You'll probably do others, but if you skip Powell's, you're insane.
As far as beer goes... Where to start? The Rogue brewpub in the Pearl is a great place, excellent beer, only a couple blocks from Powell's. Deschutes also has a brewpub in the same area; you could hit up one, go to Powell's, come out several hours later in a daze and go to the other. Henry's Tavern is also within spitting distance of Powell's and it has everything under the sun, but it's a lot pricier for some inexplicable reason. More upscale, less Portland-y.
You have to try a McMenamin's while you're in town. They're everywhere and they're all similar but unique. If you're staying downtown, you might be looking around the 21st/23rd area, Blue Moon, Ram's Head, Mission Theater, Crystal Ballroom, etc. I find those to have less personality than some of the other properties. I'd recommend Kennedy School, personally. A bit of a trek from downtown, but it's a converted elementary school with a number of different bars on the premises, along with restaurants and a theater. The architecture in the Boiler Room pub is worth it alone. Ruby and Terminator are two favorites; a Rubinator combines them and identifies you as a local (and it's damn delicious to boot, try it).
There are really too many brewpubs in town; Widmer Gasthaus, Laurelwood, Hopworks Urban Brewery, Lucky Lab, Hair of the Dog, Burnside Brewing, Bridgeport, MacTarnahan's/Pyramid, Alameda, Amnesia, etc. And basically every restaurant has a wide variety of local beers regardless. You can't really go wrong.