The ply is on the flat portion only and I installed two 1/4-20 blind nuts. The location for the new bolts is the outlined in the last item under the "Important" heading on page 2 of the general instructions. Can't help you on the drill size for threads; maybe google it? Wood thickness is a good question, can't say for sure. I think it's more that the ply extend longer up the fuse to resist the twisting pull-out force. I've never seen the wood fail on gear pullouts, it's always the glue and the gear block twists out of the fuse. Remember we're using nylon bolts with much less shear strength than steel.