I used SS "truss head" screws when I attached my deck panels, too many of the original screws were messed up and I couldn't source extras. Kind of a laborious procedure the way I did it as the SS screws had issues cutting into the aluminum. I used a 3" long steel screw of the same size and thread pitch (with the head cut) off as a "tap" to thread all the holes, then ran the SS screw in to the hole. (When the steel screw cut into the aluminum it heated up, then the aluminum cooled and shrank so the SS screws were tight.) Basically, drill a deck hole, tap it with the 3" steel screw chucked into a drill, then insert SS screw.
My boat came with the "5mph" seat base/pedestals in all positions, and still has them.... During my resto I gathered a hoard of pics online getting ideas to incorporate into my build, and all of the "Crestliner" pics I found (before 2010 or so) had the 5mph base/pedestals in all positions. My take is it's a lawyer/liability thing, and what was once acceptable may not be any longer, manufacturer liability. I overnight on my boat, and it's nice being able to pull the seats to clear the deck. If in doubt, go for the sturdier 2 7/8" fixed pedestals.
My boat was originally decked with 1/2" (or 5/8" don't remember) and I replaced it with 3/4. The aluminum deck hinges were an issue, but I kept the original hinges which do not allow the hatch to flip open all the way and lay flat on the deck. It's not a huge deal as I installed
spring loaded hatch lifts on the big hatches, to hold them open. Smaller hatches don't open the full 180*, but it's not an issue for me, they probably open 120* or a bit more. If you want the hatch to lay flat on the deck, replace them with 1" offset piano hinges.
Replacing the livewell hatches with plywood could be an issue if the livewell opening is "lipped", as the plywood wouldn't lay flat on top of the livewell. My aluminum livewell hatch (big one, 12"x36" or so) was a bit tweaked, but I was able to bang it back into shape. I didn't like how flimsy the hatch was, so I took a piece of 3/4 ply, split in half on the table saw to get a 3/8" thick piece and epoxied it inside aluminum hatch (plywood fits inside the livewell opening when closed). This made the hatch much sturdier when stepped on.
One thing about replacing the decking with 3/4" is you'll have to re-align the consoles and windshield for the thicker deck material. My consoles are built different than yours, plastic top and aluminum legs, so I was able to re-drill where they attached to account for the thicker deck.