Although Beating the hell out of it with a hammer might make you feel better. It for sure is not going to help the rail any. Sanding might not work too well either as far as keeping the the whole length of the flat bar true. You say they are divots but then you say there is a bump. A bump would be easier to deal with as you would only need to remove the metal from the bump. But if they are divots then you would have to remove metal along the whole bar to true it up. The most ideal way to fix it would be a surface grinder but thats not something everyone has laying around in the garage. Even if you did have one it would have to be a big one. Other then that if it was just a bump i would true the flat bar up in a mill and cut it off with a end mill. If it is a divot then you would have to cut the whole length of the bar and then you run into needing a big mill that has a large enough swing on the table. If your really good with a bastard file you might can get the bump down without messing up the trueness very much.
Having said all that i would put the piece you have now for sale on craigs list and just order a new piece. and maybe leave a note on the order saying you need some really high quality bar stock for your project and maybe even try to give the metal cutter guy a 10dollar tip so he would be more likely to hook you up with the best bar stock in the place. Thats my 2cents wish you luck in resolving your dilemma