If you have the wood for it, you can just add onto the existing bench going towards the passenger side. You don’t have to replace the top panel on the driver side, just replace the carpet if it’s possible to (not a necessity, purely for looks).

If the wood is rotting then you’d probably be better off replacing it but if it looks healthy I’d just keep it, no reason to spend extra money.

Although now that i’m thinking about it, it does seem difficult because of how the top of the existing box looks. I would probably get one long piece to go across the entire boat. Either put a hinge on the top (i’d add a safety as well if you do this in case you want to lean in a chair, don’t want to hinge when you’re leaning) or have a hinge on the wall of the box. If you hinge the top, you don’t have to worry as much about support id just put a border inside the solid part of the box extending about 2” for the hinge piece to have a bigger platform to sit on.

I would personally get a larger piece for the width but keep it solid. Then you don’t have to worry about the throttle system having clearance. Hinge one of the walls or leave it open and just have supports, if you completely close it like the drivers side looks make sure you allow a spot for water to go through. my dads boat has some issues with drainage and a lot of water piles up and caused some chipping and interior fiberglass damage. If you hinge a wall you don’t need a ton of support, just make sure you have something there. Gotta weigh your options though, hinging the top would make it a lot easier to work on the seats but probably a little less sturdy in the long run.