Couple things I noticed.
First was the sheething. They put it on to cover the upper corners of the openings. This is the way it shoud be. On some projects I've been on I've seen it just lined up with the outside opeing of a door or window. With the overlap, you get your strength to tie everthing together. The same aplies with sheetrock. Overlap the inside corners and you wont have any cracking. Just one of those little clues you look for in a good job compared to a bad one.
The plumbing issue is a pain, but doable. They will cut out the concrete, dig down into the dirt and replumb the lines. Then they will patch the concrete. Since you'll have some sort of finish on the concrete, you will never notice this. It's why they put in that plastic box for the shower drain. It's almost impossible to get those drains lined up exactly right from the rough in stage. What happened with you isn't uncommon at all.
The headers aren't what's normal for me. Using the 2x4 on the bottom works, but I like plywood sandwiched between the boards. Did they use plywood? Again, it's not a big deal, just a personal preference.
The archetect issue isn't unique at all. The mistake you made was listening to her excuses. When that starts, it's time to move on. Most people don't want to offend others, but when you hire somebody to do a job and they don't do as they said, they they are insulting you and if you allow it, they will continue to do as they please. I only give somebody one excuse. When I hear a second one, I won't use them again.
As your finding out, balancing your subs and suppliers is one of the biggest headaches your GC has. Getting people to the job after the materials are delivered can be quite tricky. Especially when deliveries are late. I'm working around a window issue myself right now. In about an hour I have a meeting with my supplier to get it all straitened out. Sometimes you have to go to them and have a face to face meeting. It puts you on a priority for getting your stuff. Otherwise you fall down on the list of when they will get to you.
The house is looking really good so far. One thing to watch for is how straight the walls are. Just stand along side them and look down the length of the wall. If you notice any bending or twisting, address it now. Good framers will work with the lumber they get and use the bad stuff for cut offs. This is especially important in your kitchen and any room with cabinets. I've seen some very expensive homes with walls so twisted they had to use one inch spacers to hang the cabinets. This can really add to the finish price of a home.
Same goes for that door you mentioned. Talk to your GC now about it. The quicker you bring it to his attention, the sooner he can address it. Even if your unsure, talk to him. He's built allot more homes then you have and can probably come up with a solution faster and better then you can. This is what your paying him for.
Thanks for posting all the pictures, it's fun to follow your progress,
Eddie
