Leave off the footpeg brackets and make a spacer to replace the missing brackets, or shorten the thru bolt. The internal spacers of the chaincase must remain in place.
I would make a new, shorter, thru bolt from rod stock, thread each end . That is not keeping purity, but neither is fitting rearsets. At least you will have the original thru bolt should you decide to go back.
You will need a heavy washer at each end to prevent the nuts from gouging into the serrated ends meant to be adjusters for the footpegs.
Slick