Nice work cleaning it out.
I'm not seeing the gap on the left at the transom you mentioned. And did you mean on the left in the pix, on the left side of the boat? Looking forward or aft?
Looking forward from the transom, the left side of the boat is PORT & the right is STARBOARD.
And in a closed bow boat, like yours, the change to 5/8" deck won't impact a whole lot of other stuff when you start putting it back together like it would in a boat w/ 2 consoles & a split walk thru windshield. 5/8" is a nice choice between less substantial/less expensive (1/2") and heavier/moire expensive (3/4"). But it might impact any tin trim & supports under the gunwales or splashwell down to the deck. Like the slider doors @splashwell or the side pocket/trim @gunwale. It's 'only' a short 1/8" difference, and should be manageable.
