Can a naturalized US citizen stay overseas for 1 year in birth country or any other country? Is there time limit just like GC?

Once naturalized and become a USC, there no limitation and/or restriction of any kind as to how long you can remain outside the country.

How much total fee for greencard when filed I485 together with I130, I131 I765 I864 I693 ?

It seems that you forgot to pay the fee for the I-130 petition and that is why the entire case was returned.

Do I need apply for new visa?

Talk to the new school's DSO. You will in all likelihood need to apply for a new F-1 visa.

Can we get divorced in U.S. if we are on H1B and got married in India. Will it be recognized in India?

Need to pose this question to a lawyer licensed to practice law in India.

Can i refuse vaccinations for my i-693?

You will need an experienced lawyer to assist you with filing a waiver of the vaccination requirement.

Yes, a third person can complete and file any "DS" form/application on behalf of another individual.

My fiance applied for a student visa, he was denied, reason was tense?

Important facts have been omitted here. Need more information. Can only be obtained during a private consultation.

Is there a way my spouse can get EAD after filing I-765,without giving the biometrics? Or is biometrics always a mandatory step?

Giving biometrics for an EAD application is an absolute requirement. There is no way around it.

How many biometrics do you do for adjusting your statues and employment authorization?

Only one biometrics appointment is required.

You will only become eligible to apply for the "removal of conditions" when only 90 days remain to the expiration of your GC. Not before.