Thanks for all the awesome tips! I ended up going with the edge glue method. Alignment isn't a huge problem for me. I aligned 1 edge flat with a board. I couldn't get perfect board lengths because I didn't have a stop (because I needed a workbench for the stop on the miter saw). As is, I am going to lose less than 1/8 of the table top, which I think is fairly good.
As for flatness, I am planing the edge of all of the boards using a #5 and finishing with a #7 AND using a 48-inch level. Any gaps that I see are very small and get compressed with the glue. I am flipping the boards based on grain and will eventually plane it flat. I opted for this path rather than going board by the board because the boards were actually fairly flat already. My guess is that I am going to lose about 1/8 to 1/4 inch on the board height, which is acceptable.
For the bookcases I need to build, I am probably going to use edge glue as well but dowel them to keep the longer boards equal heights when gluing, less for strength and more for ease of use. Also, I think I will use a plywood back for some serious strength and then groove the decorative board on top.