Well, many of the problems you list may be non-issues. In some areas you can run all the branch circuit runs into the panel as he did. Are AFCI's required under the current code adopted in the area? Is bonding around the water heater required? Derating? I thought you said he used all #12. Other issues such as improper grounding, GFI's etc are correctable.
What I would be concerned with is the improper service ground (this should also be correctable) and box fill (not easily correctable).
That said this is a DIY'er job and there is probably more that you are not seeing. Unfortunately the time to see and correct all of these problems was before the sheetrock was hung, now it's going to cost him big time.
Not to blame you but you did have an involvement here, not once but twice. You created the plans then during your visit, saw how bad things were and unsucessfully tried to clean things up. Red flags should have gone up with the calls for answers to "basic questions" and the fact that your father-in-law knows nothing about electrical work.
So now after the house is nearly completed you are concerned that the wiring is not safe? You are afraid that if you "blow the whistle" on him he is going to be mad at you? How do you think you will feel if the house burns down killing everybody? Then what happens if the law comes after you because you had an involvement?
I say do what ever you have to to get the mess cleaned up.
-Hal
