[makade]

Mike, just some thoughts, I would try to leave the inside alone, I don't think there is enough room to add knees or gussets. Another thought would be to do away with the lower level of the splashwell/have the deck the same height all the way back.
I think a lot of guys have done the transom from the outside-in without doing much to the inside glass. I'm sure someone will give some better details/tips.
I will be doing the same thing some time in the future. Looking forward to seeing your progress. Welcome to the sight and nice looking Mako.