How can i get a working permit

More facts are needed to be able to provide you with a meaningful answer.

Will subsequent visits with my wife could be an issue with the immigration officers. I am likely to stay for 6 months everytime.

As long as you respect your I-94 expiry date, you should be fine. Be mindful that you may not be granted 6 month stay every time.

What are my chances for applying STEM Extension?

There is actually no other options. If you want to extend, then you have to extend. You should work closely with your DSO.

Would I get RFE on 485 if I quit my job? does it make difference if I stay in US or India while working for an Indian company?

Since you got your I-140 through NIW, you can work for any employer you want. But, green card is for people who reside in the US not abroad.

What is the process to petition for my spouse who is outside USA and what documents I need to file for her?

If you are not planning to consult with an attorney, check USCIS's website.

I-539 petition got approved after re-entry in US under H1-b. How to reactivate H1-b? Would need H4 stamp if traveled outside US?

Too many questions for an online forum. You should talk to an immigration attorney in private.

If I complete master in december-2016, Am I eligible for OPT?

Too many questions for free online forum. Contact your international office.

When will I receive my green card after the marriage interview?

If you receive approval, you should receive it within a month.

Conversion from H1B to B2 Visa

You have asked bizarre questions to be honest. Talk to the counsel of record.

Yes, you need to submit 2 photos. The timing depends on the center and their workload. Check with your local USCIS office.