Congrats. I get the overwhelming part. I've been custom home builder for over 35 years. Whenever it feels like your dealing with too much, stop and think things through 1 room at a time. Can sound crazy, but you can never imagine how many times I had buyers close their eyes and visualize 1 room or 1 wall.

Few things I design standard in every home I build:

42" entry door
All hallways are minimal 43" rough
36" interior doors
If its your "forever" home, design in blocking for hand rails, grab bars, and the things that make end of life easier. think of a w3alker or wheelchair. Additionally, plan out your closets and bathrooms and put blocking in for all your accessories - shelves, towel bars, paper holders and so on

If you consider plastic windows to save a little $$, do yourself a huge favor and bump it up just a little and go with the fiberglass/composite Pella Impervia. Well worth it. frames are so much more stable than vinyl.
If your installers use big-gap foam or open cell to seal the windows and doors - fire them! Low rise/minimal expanding closed cell only

AIR SEAL!!!!! Can not emphasize this enough. $4-5K invested in proper air sealing and improved insulation practices will pay you back thousands in energy costs.

Do mechanical walk-throughs before rough in and think out room by room exactly how you'll use things. Don't accept "code compliant" When you walk into a room, where is the switch for lights...what do you turn on first, another switch for ceiling fan, are they switched separate, are the top halves of the outlets switched to turn on lamps?? Are the outlets spaced so they are accessible from your furniture layout ?? Do you need floor outlets?

Ask for a roof venting calculation from your builder. The vast majority of municipalities don't require it and the roofers/siding applicators just guess and never take 3 minutes to run the calc. If it isn't balanced, you get negative flow out your soffit vents and costs big dollars to run A/C. I've seen many homes blowing hot air down into the insulation instead of rising up through a ridge vent.
https://www.owenscorning.com/en-us/roofing/components/vent-calculator

Don't let any contractor use silicone caulk on any anything exterior. Use a urethane based caulk like Quad or Vulkem. Sillycone fails in a few years and you'll create future problems. Its cheap, so everyone uses it IF they seal their penetrations. If you need to, buy 10 tubes and have it on hand for them to use and demand no silicone.

anyways, just a couple thoughts. If you get hung up on anything, give me a shout. Be more than happy to assist

If you don't mind, tell us the cost per square foot for the construction.

An upscale stick-built home with a basement in my area can run around $206 per square foot.