1. Yes, it is mandatory to mention pan no. during registration. However do not file form 60. Since during registration only Pan No. is required not the copy of the card so it is not a problem. Moreover you can make an affidavit in this issue which will take care of everything.
2. The name of the Pan card need not be changed at all. If you make an affidavit which is a one day affiar that is enough to solve the problem.
3.Do as advised above.
Do note that due to anomaly on name of your wife, there is no provision to charge extra 1% TDA. The builder is misguiding you.