Options for me at this stage

i) She is living with me separately at Delhi now, with no Contact of her from my parents, sisters or any of my relative. I am in the process of making ID and address proofs for her from delhi. However, i am remaining in contact with them. Can she still file a case against them, and if she does so, will it stand in court of law or Police station. My parents have still not disowned me.

Even if she does not have contact with them directly, she may implead them as parties in DV case and co accused in dowry harassment case.  If she does so, then you have to move appropriate courts to strike off their names.  In the meantime, even though it is not a full proof measure, your parents can issue a paper publication disowning you.

(ii) If she files a case against me in near future, can i apply for Anticipatory Bail at delhi, even if she files a case at Aligarh. Mind that there is no provision of Anticipatory Bail at U.P.

You can file anticipatory bail in delhi ancipating her filing complaint in Delhi.  But if she files complaint in Aligarh,  A.B. from Delhi is not a protective measure.  If you get AB and if they arrest you from your Delhi home without taking Delhi police into confidence and without producing you before the Delhi magistrate, it is irregular and illegal on their part, but they will show your arrest beyond Delhi boarder, i.e., NOIDA etc.  By the way, without any complaint before CAW cell, it is difficult for you to get AB from Delhi.

(iii) Arriving at a mutual agreement on all the issues, giving all the streedhan to her, taking her stamped receipt and getting it notarised on stamp paper. Will it be of any help at this stage, if she files any case in future.

Yes.  But you should do it in the presence of two witnesses, who can come to court and give evidence, if the necessity arises.  If they are your neighbours and not relatives, their evidence will have more weight.  Also, video record the entire process of handing over stri dhan to her.  If stridhan is in Bank's locker, take her to bank and let her picture come on CCTV and get herself signed in the locker register and allow her to carry her jewellery while coming out of bank, which will come in CCTV.

(iv) Knowing the fact that she has people with political background in her family, what precautions should I take, and what proofs should I collect in my favour to safeguard me in my near future.

(v) As she is into affair and adultery outside marriage, for last two years, and still continuing, can it be base for annulment of marriage as she hid basic facts, and since committed a fraud. Also, she hid about a disease(PCOD) which she was having since very beginning, and which came to light when she was taken to doctor. i have doctors prescriptttion from AIIMS.

Google is telling the PCOD is not a serious disease and hence, on that ground you will not get annulment.  If you can prove fraud on account of her pre marital affair(very difficult I say), then you can go for annulment.  But, post marriage affair also is called adutery and on that ground, if you can prove that ground, can get divorce. if you take any action, better prepare for facing S.498 A and DV case.

@Adv Chadrasekhar Ji...

Thx for the advices, also kindly enlighten for point number iv.. What all can I do to safeguard me and my parents from false 498A and DV cases. Also, if I am able to collect evidences like(photos, may be videos, Call records i am already having) will it be of any help. And based on this, if I file for divorce or annulment, how much time will it take to complete all the proceedings in the court.

In Delhi, it is about 3 years for finalization of annulment or divorce case.

@ Author 

There is no hard and fast rule that if you file for Divorce your case would be over in 3 yrs time as stated by our friend Chandu . It takes years maybe 5-6-7-10-12-15 yrs . And for every action there is a equal and opposite and equal reaction like 498 or DV and all that can be done is to contest these false cases and gather as much evidence as possible .