I wish you the best on your exciting purchase. It will be a long winter waiting but exciting as your new yacht comes together.
I bought a 44 DS in 2007 at the boat show in the Fall so my experience was exactly parallel to what yours will be. Let me say right up front the boat has been great with no issues to speak of, my dealer was terrific, and Hunter has been also great. I couldn't be happier with the design, the systems, and the sailing and powering performance. Here are a few thoughts:
1. We had two coats of epoxy applied to the hull before bottom paint was applied.
2. I made a conscious decision with the full enclosure to have the dodger at the same elevation (as close as possible) to the elevation of the bimini so there is an unbroken line visually from the forward end of the dodger to the aft end of the bimini. This gives you the maximum height overhead when standing at the top of the companionway. I am 5-11" and I can stand under the dodger on the bridge deck with almost full height. I also had the bimini extended aft to cover the perch seats, even though they are outside of the full enclosure. also, be aware of the various supports holding up the bimini on the arch. Your canvas guy may want to place a support where the side curtain is for ingress and egress from the cockpit. This is not desirable. I also had grab handles placed outboard on the dodger for support when moving up the side deck. I also had "blinders" made to cover the dodger eisenglass when at the slip.
3. Maxprop. The key here is getting the pitch right. Recommend talking with PYI on this. Mine is set at 15".
4. I installed a salt water washdown for the anchor locker.
5. I had the dealer install a mast head tricolor light for running offshore. This and the washdown required the installation of an auxiliary blue sea DC breaker panel as there were inadequate spares on the stock panel.
6. Davits. Did you order the Hunter davits which mount on the arch? That's what I have and they are great. I diod add various features to keep my dink from moving around in a seaway.
7. Recommend running the AC condensate drains into the shower sumps fore and aft as I have. My bilge is always dry.
8. Batteries. My boat came with 3 x 4D gel batteries. Some are delivered with 2, but wired for three. Suggest you look into this.
All I can think of right now. If you would like some pics, send me a private note with your email and I'll send them along.