[dcobbett]

I agree with Fellowship, except there is an alternative that may work for you. Run them through the transom now, but keep the holes to the outer edges of the transom (minding the top flanges to the tab brackets). You can also keep the through the deck scupper holes operational if you want.
After you rebuild and raise the deck, you have options. You can either plug the holes in the transom and drill new ones, in which case I would suggest that thet be closer to the centerline than the initial ones, or leave the initial ones where they are and just install new piping to them from the "higher" outlet holes in the new cockpit. This should work, assuming you don't add a lot of new weight in the rear of the boat when you re-do the deck. In the alternative, when you raise the deck, plug the old transom hole sand drill new ones closer to the boats centerline to avoid overlapping holes.