Doing the postscript file would probably be the way to go it seems. How exactly does that work? I am just the printer, we have a prepress that sets the files up for me and I take care of them from there. I know the page exceptions are going to be pretty random.
If they are truly random, the only ways are your manual way and my way lol that I know of. is there a way to do it inside a pdf? regardless it will take awhile.
Prepress will have to do it... or Whoever is making the files has to program the variable stock to pull pages when needed based on whatever data requires the page. Postscript, this info can be included in the file. Hard to explain if I dont know the print production system they use.... It has to happen when the print file is generated. also depends on what you need printed on that page.... WE use GMC to add personalized data to background, page color callouts for output.
I don't think that will help you though I'm afraid, at least in the short term. Thats years of us just figuring it out.....
Best i can think of is, if its a giant pdf and you have to do it:
open pdf in adobe, separate files into smaller round number chunks of pages. get a small file going using the freeflow exception pages entry. Then at least your machine is running while you prepare files. Pick a good round number so the math isnt too bad.
even better, is if your prepress cant do the multiple page pull, have them send out smaller numbers in each file. so you can maybe setup 5 exceptions at a time.
FOr instance, we generally break"regroup" files into 500 pages anyways. for handling/cutting....etc