Not to late and exactly what I am planning on doing, at least for the brackets. I'm going to clamp the drill vice to the table and then clamp in a stop so that, for example, the top left hole in every bracket is in exactly the same position. Then I'll move the vice and drill all the bottom left holes etc etc. I'll always reference off the same side of the bracket so I should end up with all of them exactly the same.

For the framing I'll certainly batch them up and mark them together, I'll have a think about how I might make a hole transfer jig though as that could really speed the process up.