You are creating a lot of extra work for yourself - YOU don't have to actually change all the elements of each colour to black. Just make sure each colour is a spot colour & when you print, tell the printer to print the job out as separations and, voila, each of the colours will print out on a separate page - in black. You will need to print out registration & crop marks on each page so that the silkscreener can register the colours properly.
I remember seeing someone create a job with 3 colours, make 3 copies and then delete 2 colours from each copy so that they ended up with 1 file for each colour - then changing all elements on each page to black. A complete waste of time - let the printer do the work for you - more accurate and much faster.