The existing gudgeon screws on my old H-16 were #12 (don't know if that varied over the years). I was able to tap out the stripped holes in the backing plate to 1/4 inch (slightly larger). If you don't have any sheared screw parts still in the backing plate, you may able to do the same and avoid relocating the gudgeons.
Regarding the deck lip, I'd seal it with a coat of epoxy to minimize water getting into the laminate, then forget about it.
Thanks for the tip. Hobie sells a set of 16 nylon locking bolts for this. Not sure what diameter they are. If I have to offset the gudgeons I'm hoping there will be enough adjustment in the tiller bar to make up for it.