Can I visit to India and reply for RFE after that ?

That is a risky move. You should speak to the attorney handling the case before you attempt this.

It wouldn't hurt to have a certified court document stating that the charges were dismissed so if this comes up you can prove the same.

Will the government separate me from my children and deport me? Can I apply for renewal or permanent citizenship? Can I legally

If your misdemeanors are CIMT's (crimes involving moral turpitude) which they likely are then you will get yourself put into removal proceedings if...

Will I have merit to ask for some of the rent back? If so, how much?

Since you willing lived in the house with the second hand smoke and paid rent I don't see how you could now fight to get that rent back. You never...

1. Port of entry with live visa from old employer? 2. Is it common to revoke h1b petition when employee left the job?

You have to use your current visa. You can't use a revoked visa to travel. I'm not sure if I understand your question.

Petition for Alien Relative

A separate petition would be needed. The wait for your sister will be much longer than that for your parents.

Can i file seperate tax returns? if i do will that be pose a problem in removing my 2 year condition?

You have to file married but you can file independently but married. Married people file independently for tax purposes all the time. As long as...

Person with no work authorization is working

Why do you care that his guy is working in the US?

If my i-134 sponsor's income doesn't meet requirement Can he use his property? How?

Technically yes but it is complicated. Getting a joint sponsor would be much easier.

I have an asylum interview pending. How my children can get SSN?

They get a SSN the same way you would by applying for it with EAD. If you speak to an immigration attorney they could help you with the process.