1. As per Section 6 of Hindu Minority and Guardianship Act, 1956, custody of child below five years will be with mother with visiting rights to father and custody after five years of age will be father with visiting rights to mother. Though this is general rule, this is not fixed law, in special circumstances child above 5 years especially which the child is girl custody is given to mother with visiting rights to father. 
2. There is no preventive vaccine against criminal prosecution. Any agreement/undertaking by wife not to file criminal complaint will go against you as the question will arise why in the first place you need such agreement/undertaking, it will lead to doubt that you are planning some offence against her. Best option is not to give her any excuse to file any cases against you.
3. There cannot be any defamation against complaint to Court or higher authorities. Making allegations in complaint against accused is not defamation.

Now that your wife has withdrawn the cases and returned to your home, it is better to move on. Do not have any imaginary fears of false cases being foisted against you in future.

File petition for quashing of FIR based on settlement arrived at with wife 

2) don’t file any defamation case against wife 

3) custody of daughter is generally awarded to mother 

4) you can seek joint custody of your daughter 

Dear client, 

Unfortunately, there is no such measure you can take to defend yourself. However, you can file a case of defamation against her for filing a false 498a case against you. And you can apply for your daughter's custody but up and until the case is resolved, there may not be higher chances of you receiving custody. Please consult with a professional lawyer for more advice.

Thank you. 

- If your wife is agreed to return to you , then take her consent for withdraw all the cases filed by her 

- However , for quashing the FIR , you can approach the high court on the settlement ground

- If , your parents will file any case against her , then she may not give her consent for withdrawing the cases. 

- Further, as there is already FIR against you all then in that eventuality defamation case is not maintainable. 

You can file cases against her only after you get acquittal. You can contest the cases filed by her I'm court. You can take anticipatory bail to secure from arrest

If you have filed a case seeking restitution of conjugal rights from her, this clearly indicates that you have condoned all her misgivings or misdeeds of the past.

Bear it in mind that law cannot give you protection agaisnt her filing any false cases in future,

you may have to challenge them when it occurs again.

Also no defamation or intimidation case would be maintainable because she had lodge a criminal complaint with the police, hence  it is the police who had prosecuted you and not directly by her, hence no case against her is tenable in law,. .