OK, I've got a few minutes so I'll try an answer some questions here.
First a few disclaimers....
1) If you can't make decisions on important subjects and just generally like to coast by things. Don't build a house.
2) If you are building with a S/O and the two of you have...differing...tastes in things and have troubles agreeing on things. Don't build a house.
3) If your marriage/relationship is already sort of shakey. Don't build a house.
4) If you don't have a pile of excess cash (like 10% of your contract value) laying around. Don't build a house.
5) If you don't have a good backup place to live for 2-6 months past your expected completion date. Don't a build a house.
Ok. That being said, if you can work around those "gotchas" then it will be one of the most interesting, rewarding things you'll do for your family.
There's a pile of things to consider when building. There are three primary things you'll have to address.
1) Where you are going to build. What is the layout of the lot? What size or style of house will fit on there? What utilities are provided? Natural gas, water, sewer, and high speed internet? What is the school district like? What special covenents/HOA rules apply? What is the neighborhood like? How are the property taxes on the type/size of house?
2) What do you realistically need, and what can you realistically afford. It's very easy to get into "ok, that's not that much" game when you are talking $1,000 or $3,000 or $5,000 upgrades when you factor it over the course of 30 years. But they do start to add up. Figure out how big of a family you plan to have, and add a bedroom extra...just in case. It can be an office or toy room or something in the meantime. You never know if there's a random chance of twins or an "oopsie" kid that slips past the goalie when you thought you were done. It's cheap to add the space now and have to "trade up later". However big of a garage you thought you needed...make it bigger by 2 feet every direction...ect. Come up with a realistic plan of what you want and need.
3) Now...who's going to build it? That's the most important part. You are going to be in bed with your builder for the next 6 months or more depending on size and building practices and weather. This guy is responsible for the place you are putting hundreds of thousands of dollars into, and plan to spend a significant part of your life in. Interview...interview...interview. And follow up on as many references as you can. You'll quickly learn what builders have good reps and which ones don't. Talk to the lumber yards and trim providers and see who's good about paying their bills. Talk to the masons and see which ones are good to work with. And most importantly get a list of people that have built with the builder...preferably recently and long term and see how their house has held up.
You'll find that there are three types of "builder".
1) Really no customization at all. Basically they have a house they like to build. It's a specific size. They do everything their way. Everything you add is either unavailable or a major upgrade cost. The only choice you may get in things is the color of the carpeting, counters, cabinets and fixtures. That's it. You basically walk in and say "I want this number of bedrooms and have this amount of money" and they turn around and show you what they are going to build.
2) Semi-custom. In this situation you have much more control over things, but the builder is still working from a "known" plan. You'll walk in to their office and say "I think I want a 4 bedroom, two story, and in this price range, but I've got some specifics on the room layout and sizes". And they'll go to their plan books they've done in the past and find a good starting place and start working with you to move around a bathroom, or make a room bigger or move a closet or add a walk in pantry, ect. In this situation you'll likely have much more control over things like room sizes, ceiling heights, construction materials, choice over all items like window size/placement, fixtures, sinks, flooring, cabinets, doors, wall finishes, ect.
3) "True" custom builder. In this situation you'll walk in and the builder will say "What kind of a house do you want me to build you"? The sky is literally the limit. They'll sit you down with an architect or take plans from one that you've already worked with and literally leave almost every singe detail and option up to you. If you are a first time home owner, not familiar with the construction industry, or just generally are not a detail specific person this situation is very overwhelming. And not cheap.
I went with option "2" after interviewing and doing some rough drawups and quotes from the other two types. My General Contractor was 81 years old. He had been building homes since 1950 in our area and had an excellent reputation among clients and sub-contractors.
In our initial interviews we came up with a basic floor plan, a good layout of upgrades and options wrote in what responsibilities we though we could take on. The contract came out to be around $342k. We signed the "intent to build" contract on October 31st 2009. It took almost 6 weeks to get the building permit ready and by then winter had settled in for the season.
We didn't break ground until the first week of March, 2010. We excavated and poured footings and then were promptly shut down that week for another 4 weeks because the road commissioner shut down the roads to heavy equipment. So it sat for another month. And then my mason got pneumonia and we waited another couple weeks for the basement to go in.
We didn't actually start framing the house until the middle of May, 2010. Almost 7 full months after signing my contract. Framing lasted through the beginning of July. Then the finishing indoors finally wrapped up and we moved in the last week of October. A full year later. It's now July 2011 and I'm just now getting a yard growing.
During the build process I was talking to my general contractor almost daily. Asking what I wanted done with this or that, that I needed to make sure we picked out this or that item. Asking me to call this or that sub and make sure they understand certain things. I spent A LOT of time on the phone and on the site. It probably consumed clsoe to 10-15 hours of my time per week just babysitting and supervising things. And that's even with a general contractor handling a bulk of the building and issues.
There were a lot of judgement calls we had to make even after the inital drawup of the house. Our builder did complete "stick built" homes and did not use pre-egineered trusses for the roof. There was one week where the front elevation of our house changed 3 different times in drawings between the framer and the contractor before we finally settled on what we ended up with. Closets got added. Hallways got widened. Attic space was framed out. Ect.
Our builder let us do a lot of work on our own to save on some costs. My Dad did all the brick & stone work on the outside of the house. We did all painting including trim, walls, ect. I did all of the hardwood flooring. I also did the radiant flooring in my basement as well as the low voltage stuff like networking whole house audio, and the whole house vaccuum system. I also mudded and tapped my garage (UUUUUGHHHH!!!!).
Even doing that we still went over. Windows were $1000 over budget. Our electrician bill was $2,000 more because of added can lights, outlets, switches, and extra runs to places not originally planned. We added a roof over the deck for another $5,000. The framing changes to closets and walls cost another $3,000. Upgrades to things like stair hardware, trim, and doors cost another $2,000. The well was another $10,000 more than planned. Ect. We ended up going over the contract price by like $20,000. And that's even with paying close to $20,000 in flooring, lighting, and well costs out of pocket. As I said...make sure you have a slush fund well in excess of 10% of your contract price available for run-overs.
And that's also not including costs that the contractor ate. Our foundation went $6000 over budget from what he planned. He ate that. Extra permits and engineering cost $1500. He ate that. There were a number of other little things that added up that the GC had to pay out of pocket/his profit to get the thing done. A lesser contractor would have passed those costs onto the buyer unless they seriously fought it.
Almost 2 years later sitting back and looking at it....if you asked me if there are things I'd do differently I'd tell you "absolutely". And if you asked me if I'd do it again I'd tell you the same thing. The level of appreciation you have for the place is so much higher than picking a place out with a realtor and "making" it yours. This place you literally did have a hand in making.
A few things I would have done differently...
1) Made my garage bigger. It's decent size...but I still want another 2 foot wider in each direction.
2) I wouldn't have picked up a paint brush. Painting sucks. Trim painting sucks even more.
3) I originally wanted a ranch. Went with a 2 story. Would still rather have a big ass ranch than a tall 2 story.
4) Would have spent more time working with an architect or just my own skills setting up the house on the lot and layout a better. It works, but there's some things I would have adjusted. I just didn't have the vision up front to think about it.
5) I would have put radiant heat all the way through my house...main floor, garage, ect. Works well with a ranch. Not very practical with a two story. Conventional forced air works...but I'd rather heat the floors.
6) You'll find with houses that pricing works in a tier system. Pay one price and get XXXX sq ft. Pay more and get the same sq ft and more finishing details. Pay more and you now get XYXX sq/ft and the same finishing detail of the previous class. Play XYYY and now you the same sq/ft of the last tier but more finishing.
With mine I went up in sq/ft but not to the next level of finishing. So I've got awesome sized bedrooms but the level of luxury isn't the same as other houses in our price range. It's easier to add finish quality than space later on...but that's not something that is always noticed by other people looking at particlar price ranges. Our interior fit and finish is not up to snuff with how fancy the house looks from the exterior. It's not bad, but it's not what many people expect from a $400,000 house in our area. On the flip side, our bedrooms are sometimes twice as big as other houses in our price range. So that's something to keep in mind.
Only other advice I can give you is to take your time. Figure out what you really want, do your homework on builders, and ultimately build the house that *YOU* want.