If it was me I would try and restore the original colors... i have always really like that paint scheme.
I'm surprised on the big square holes where the scuppers were, not sure why Malone did that... I would glass the holes over and start fresh with new holes for the new scupper/s.
For first time glass work i would start out with 3/4 to 1 1/2 glass mat. Then move on to heavy mat if needed when you feel comfortable with glass work. 3/4 to 1 1/2 mat is a lot easier to work with then heavier oz, but you will have to put on more layers of glass to get the same strength as something like 24oz biax.
I would fill in as much of the tray as possible with closed-cell foam and then when your all done with the glass work in the tray, pour some 4Ib foam to lock everything in place.