Why do it in one go? Just measure well and mark the individual pieces. If you use a drill press, they should all match up.
If you are determined to drill them all at once, then I would use deck screw to temporarily fatsen them together while you drill, it should prevent any movement. Or use something strong like gorilla glue (heck, even elmers would be okay) and clamps, once the glue sets, then you can drill and reinforce with bolts. Don't have clamps? Use glue and scerws and then once it all sets up drill and put in your bolts.
Best regards,
Bruce Mitchell