Cuddy Deck Repair

[mccrum187]

I know several members have attacked this problem from top-side. I was given this boat. I found that the transom had some rot and the engine required lots of repair. So with the engine already off, the transom repair seemed like a good move. The PO decided to replace the transom at some point and hacked the cap apart at the rails. I removed the cap to splice together the transom cap and the rest of it. So, that is why I have my cap off.
Further investigation showed the cross brace under the cuddy deck was rotted and split. The cuddy cover slide rails had the bolts run through this wood and that is where the rot started. I also found that every hole in the glass for a fitting had rotted wood underneath. So, I ripped off the glass on the underside of the cuddy deck to find nothing but saturated, sopping wet, rotted plywood.
The boat that Mark built....
Anyway, I would love feedback, commentary, suggestions.
I don't know why Wellcraft used 6" squares of plywood. Can anyone speculate? I think it would be easier to fit in small chunks rather than a sheet. I am also thinking about incorporating some crown into the deck to shed water. The deck was dead flat if not sagging some before I removed the cap.
I currently have all the wood remnants and high spots ground down. I have patched all holes in the top-side. I am at a point to decide to whack up a bunch of plywood or use a single sheet. Can anyone give pros or cons for the small chunks? I will do what Wellcraft did if I can't find a reason not to.
Thanks for looking.
Mark