Modifications:
-I decreased the beam of the boat by 3" (fairly easy with a GF).
-I lowered the sheer by approx. 2-1/4" to align with the lowered transom (for 15" shaft outboard).
-I lowered the mid and rear seats by approx. 1-1/8", and the front deck by approx. 4-1/2" (2-1/4" below the now lowered sheer).
I also substitued 3/8" for 1/2" ply, but will strengthen some areas to make up for it.
After making these changes, I was able to change the nesting to 3 sheets of 1/4", and 2 sheets of 3/8", including rubrails. I will also be using the scrap ply to make cleats. Below is a shot of the nesting.
For the 1/4" ply:
Note the extra 1/4" clamping board.
For the 3/8" ply:
Note the extra bow transom.
In CL's build, he mentioned the flat that was created due to the long side butt blocks. To minimize this, I removed some of the butt block, leaving just enough of the upper side for attaching a cleat:

For the stern transom, because I am only using 3/8" ply, I added an extra 1/4" clamping board. I also put one layer of tape below the clamping boards where the transom is only 3/8" thick so that it will have glass on both sides. I'm not sure if it was necessary, but I wanted to compensate since I am not using 1/2".

I made the bow transom out of 2 layers of 3/8" since it will probably see a trolling motor from time to time. I'm not sure if this was necessary either, but it "felt right" to have the extra strength their. It definitely helped when putting in the temporary screws. Speaking of that, it wasn't very difficult to bend the sides to meet the bow transom. Maybe this was due to the lowered sheer. And once attached, the angle is significant enough that I didn't have to open it back up. I brushed in the epoxy, filled with epoxy glue, and then taped wet on wet like CL did.
I will not have enough epoxy to glass the inside bottom of the boat, so I used the butt block per the plans (instead of a FG splice, which would be my first choice if I had extra epoxy/glass). It bothered me at first, having a butt block in the middle of the floor, but now that it is in place, it is not quite the distraction that I thought it would be. (It is only 1/4" ply, tapered nicely on each end, which is small compared to the ribs in the bottom of most aluminum boats that I fish from.)
Attached are two pics of the rough assembled hull. No cleats yet - the seats are sitting loosely in place.


Since these pics, I have all of my cleats cut. I hope to glue them in place and install the rubrail soon...