You've got the right idea. With a boat this long (with PARTS this long), a small error on one end can result in larger error on the other - You just do what you need to do to fit the parts. For example, if you've lofted and cut out the shelves for the boat and boat sides match and are fair, then you may have to do a little adjusting on the shelf molds and transom slot to make it all fit. For example, place the shelves in the molds, forward tips clamped together and in the transom slots as described in the manual (for order of events), but nothing epoxied yet. If the shelve molds are a little too wide, then it could be that with the forward tips clamped together, the aft ends don't fit all the way into the transom slots. The forward tips together and the fit in the transom are the bottom lines here, and you should do a little trimming on the inside edges of the shelf molds to let the shelves go where they need to while they are supported in place. And as the manual suggests, if the joint at the forward tip doesn't fit just right, run a saw through it to remove wood on the tighter part of the joint and move the tips together again ... repeat if necessary to create a nice joint at the bow. Clamp or screw the tips of the shelves together there, then attempt to fit the aft ends of the shelves into the transom ... adjusting molds as necessary. If the shelves are a bit wider than the slots in the transom that were made for them, then ... adjust the slots in the transom until there's enough room for the shelves. Don't epoxy anything into place until the bow end is correct, the shelves are all properly supported (vertically) by each shelf mold, and the aft end of the shelves fit the transom slots nicely.
Brian
