Carpet pad - don't cheap out on the pad. They offer lifetime memory foam pads these days. Get a good pad and it is an automatic upgrade to whatever you put on top of it.

Wall/Ceiling Insulation - depending on your local jurisdiction's minimum required R-Value it may only add a small amount of money to upgrade your insulation to maximize your R-Value in the existing cavity. Do it, it will pay itself back in no time, and increase the comfort of your home. If you do your own insulation make sure you research some tips and tricks to identifying common "holes", behind outlets, inside corner framing, etc... To keep an eye out for. Again, doing a simple task superbly will result in very tangible levels of comfort.

Windows - I'm not sure if they've improved but fancy windows with special insulating gases used to be more hype than substance. It seemed the gasses would eventually leak out and then you just paid extra for a normal window. That being said, the window package will be expensive. I'd look into options that have a colored or paintable surface. You don't have to have white vinyl windows. It's a small thing but it's those details that can set a house apart. Also, in the bathrooms do some research on how obscure your windows actually are, particularly in the dark. Most are very much less than modest. You might consider wider but shorter "transom" style windows in the bathrooms particularly if you have visibility from neighbor lots.

Crawlspace - trust me on this one, but if you spend some money pouring a "rat slab" in your crawlspace it'll allow you to keep that space clean. You can then use it for storage, or not have to worry about getting nasty dirty if you need to maintain something down there. If it were me I'd consider adding a few inches to the foundation walls (going deeper) and have that slab down there for storing tubs, etc... It'll keep your garage cleaner. It doesn't have to be anything special, no forming required, no rebar, and just a quick screed finish, it shouldn't cost that much to do, but it's a good add. You may as well add a light or two down there while your at it. Also, you can either hang your joists down into the crawlspace or set them on the sill plate. Hanging them into the crawlspace gives you fewer steps into the home, and is in my opinion a better look.

Backing - make sure you give some thought to backing for towel rods and tp holders in the bathroom, the TV bracket locations, coat hangers at the door, where the door knob may eventually make contact with a wall, handrail for the stairs, etc... put some thought into it up front and you'll be happy you did.

Thicker drywall and sound insulation - it's usually not a significant price jump to go to 5/8 gypsum board from 1/2". It may not seem like much, but it provides for a bit more solid and quiet wall. Also, consider walls that you may want sound insulation in, bedrooms, etc... If you are planning on keeping the master downstairs I would look at what you can do to provide an acoustic break in that ceiling. There are some strategies and for a small space it shouldn't add too much cost, but again will be great when it comes to having people above you.

Squeaky Floors - a little attention to detail will help you avoid squeaky floors. Do a little research into what to look for when installing the hardware and joists. There are some tricks to making sure they don't squeak in the future. Also, screw your plywood down instead of nail it. It takes more effort but you don't have to worry about a squeaky nail.

Exterior electrical outlets - give some thought to this as well. It seems like I'm always struggling to find a good outlet for Christmas lights, patio lights, electric yard equipment, etc...

Rough in for solar/cable, etc... - some jurisdictions require it now, but if they don't, it's still a low cost good idea. Make sure there are conduit pathways for solar just in case you decide to go that way in the future, it makes for a much cleaner install. Sucks to have conduits running on the exterior of your house if you could have just thrown some in when building. Give some thought to where you'll put your TV and make sure you have conduits and power there at the location ready to go.

Doors - I would look into the cost to upgrade to solid core doors. It may seem like a minimal difference visually, but again it'll provide for a quieter home and will have a much more high quality feel.

Paint - pick something that is washable. Especially if you have kids. You don't want to be scrubbing the paint off the walls.

Electric/gas appliance hookups - I would bring both electric and gas to the range/oven, water heater, dryer locations. If you go solar you'll want the option to use as much electric as possible. But without solar gas is the way to go.

Appliance management in the kitchen - I HATE having stuff on my countertop but there really is no place for some of these appliances. Like mixers, microwaves, air friers, ice machines, etc.... You've got a good pantry right there. Think about putting in a counter with outlets in there to hold some of those lesser used appliances just to get them out of sight. They are so hard to find a place for.

None of these are sexy upgrades, with the exception of the windows maybe, but they will all give you a more comfortable home with less headaches. Some will cost more than others. Some will provide a larger impact, and it's not necessarily tied to bigger dollars. I'd look at costing out all of them and making a decision. There are a ton of tips and tricks out there if you are doing work yourself to help you come up with a longer lasting quality result. Tips such as glueing your interior trim joints, back priming your exterior trim and or siding, shimming drywall to get a straighter finished surface, etc... Tips that separate high end builders from production outfits. Most don't take extra money if you are doing them yourself, just extra time, so you'd pay extra to have someone else do it. It's one reason why it takes longer to build a custom high end home.

I admire your ability to sacrifice to get to where you are at, it's about to payoff big time. I'm a bit envious.
Congrats, and good luck!