I picked up some materials saturday and been doing a bit of what you describe.
Got some glass strips 3inches wide, glassed on an outside overhang to the bottom edge. The bottom edge of door is 3 inches higher than height of old deck height & scuppers, new deck height will be another 2 1/2 inches higher than the bottom of the door & the door will have ramp up to the new deck with about a 30 degree pitch to the ramp so water coming in won't be an issue.
Made up side inner stops for the sides and the lid I glasses in a channel that locks over the top edge of the transom door.
The door rattling definitely won't be a problem and the bottom will be water tight. I'm more concerned about the latch itself rattling.
Ronnie,the latch starrfish posted is the best you can get.....i have ordered them thru Kellog marine supply...it is about 180 wholesalehere is one that i have, it locks when closed so vibration or a foot will not open it, you need to pull a spring loaded pin that the handle pivots on in order to open it.
That's it !
That's the one Ruby Belle has.
Who makes it ???