What about just a stainless sheet for now?

Minimum clearance from gas top to combustible typically is about 30"-36". So, no to the 18" to wood shelf. From a cooking (Chef's) perspective, spices should not be near heat. To the side OK, but above, especially gas, it's a no no.

I'd get a couple decorative plates or trivets or doodads and just stick them over the holes.

Do you still have extra tiles from that backsplash? Those tiles can be removed & replaced.

One inch? I would just fill it with grout the color of the tiles.

Melt a crayon to fill. Just like a furniture touch up crayon. And hope your new hood does its job to duct out the excess heat properly.