Re: Bunch of questions replacing wood up top.
If you are re using the wood or using the old wood to make exact copies of the new parts you can use the same holes. Look closely at the existing holes for evidence of water intrusion. Many times it makes sense to drill out old holes with a larger diamter bit, fill, and then drill new holes in the center of the fill with a smaller diameter. This seals the site of future water intrusion from the core (your boat has a cored deck and solid hull). If you use new holes that is fine too, but still fill the old ones.
Thickened epoxy works well for this, I have used cabosil with good results. Dental syringes are very handy to use to fill holes.
Think about saving your old wood parts if salvagable. I have found new teak to be very expensive, and not as good as the wood on these old boats. You might be surprised how old weathered teak can be brought back.
Your hatch covers look good. You can coat the underside with almost anything since it will not have UV exposure. Epoxy, paint, varnish etc. Keeping the top looking good is another matter. Water will stand on the surface, lots uv exposure and lots of abuse since you will be sitting and standing on them. I never found a perfect coating, but Cetol worked better than most. My boat now has plastic hatch covers.