You can get close before joining, but leave at least .010" or so incase you don't get the seam perfectly flat along the whole length. I use the masking tape joining method (stick a strip along the seam on the show face, and a few strips stretched across the grain to put some pressure on it, lift it up like a tent, squeeze glue in the seam, drop it down, and put some weights on it), which gives you the opportunity to press down on both sides of the seam with your thumbs to align any areas that are off. But still need to sand/scrape a little bit to get it perfectly flat.
As for thicknessing, I've always done it with hand plane and scraper. I usually use a toothed blade in a block plane (just a regular blade that I ground 4 notches into with a dremel cutoff wheel), and a card scraper. Cheap as can be, and a good workout
But do wear a dust mask. It's a lot less dusty than sanding, but still probably not healthy to be breathing on a regular basis.Here's a recent thread with lots of other recommendations on hand thicknessing tools http://www.luthiersforum.com/forum/viewtopic.php?f=10101&t=42486
Alternatively, you could build your own thickness sander. A few people on this forum have made them, although I don't have links to the threads handy. But you'll either need a dust collection system (i.e. still expensive) or to run it outside... which would probably mean hauling it in and out whenever you need it, which would probably be more of a pain than hand planing the stuff, which is why I haven't built one.