1) How can I protect my father and get him out of custody/jail.
First obtain anticipatory bail and then challenge the false case in the trial court.
2) How to handle local PS harassment, we also got statements from them why we have put reed petition and having an own house we should not mess with area police etc.
If the police harassment is continuing then you may move the Dist SP of police with the details and seek its intervention, a copy of this complaint may be move with the State police chief too and if necessary you may move the state human rights commission too in this regard.
3) What action I can take against my ex-wife and her associates, Is there any valid cases I can put on them.
For the present you should arrange to come out of all her false cases and then plan to file counter cases including defamation cases for malicious prosecution.
4) If we have some strong genuine evidence which includes her adult chat and obscene pictures and video calls over skype/viber etc with her boyfriend from the phone she used which I have given to her, Can any action been taken against them as currently they are trying to manipulate evidence against us and threatening my parents to put false cybercrime complaint.
On the basis of the said evidences, you may lodge a complaint against her under section 497 IPC for the adultery offences, but this can be lodged agaisnt the adulterer only and not agaisnt her though this will certainly make an impact.
5) In case bail rejected and custody granted by court, what other options I have to protect my father/family.
If the bail application is dismissed move high court seeking AB, youmay get it.
6) With all this I am not expecting area PS support, In this case from where to get help.
How can I get my child custody?
Youy have to file a child custody case under guardians and wards act seeking custody of child.
7) Please advise if it is ok to share above matter on social networking, to seek help.
It is not advisable.
8) Can new CI request for taking back custody option to court.
You keep trying the AB before police moves for arrest and until then let them be underground.