I've done this a lot. As bigbadjon said, you need to hand select each potential shaft. Look for straight grain (no sharp run-offs), avoid knots, and choose the straightest ones at the get-go.
Back home, you'll need to straighten your dowels. For softer woods like poplar and birch I use the finger ring of a pair of chrome scissors, firmly rubbing the offending side of the shaft, compressing wood fibers to curl the shaft the opposite direction, not unlike the way you'd curl a ribbon to put on a gift. Harder woods, like ash or oak, must be heat straightened to hold.
Next you'll need to spine test them. You can buy one or you can make one. Once you know the spine you need for your bow, bring a representative known spine shaft with you to the hardware store. Select the dowels that are closest.
Sorry if this sounds like ... a project. It is. It's in large part why purchased shafting isn't cheap. My best advice is: Don't short change yourself on arrows. They are the other half of a good shooting bow, in fact they are the greater half. It can be done with dowels but you need to be selective and you need to spine them.