i haven't read all this but here's what I did..
1. unscrewed the original screws holding the ply on, he'd siliconed the rest to keep it in place, scraped this off.
2. used self tapping screws and countersunk them into the ply so the ply is smooth ready to carpet it,
some people use screw caps and screw the wood on after it's been lined, i decided i didn't need to get behind there again (maybe change my mind but there's nothing behind there any, so i'm just covering the screws with the carpet.
i've learnt about different screws this last week.
if i remember right - self tapping screws are the same width all the way down which means they cut their own thread through the wood
normal screws are narrower at one end meaning they aren't held all the way through and can fall out easier.
countersunk screws have a flat head so when you cut the wood lower its sunk into the wood and sits flush.