Physician applying H1B under cap. Will my application fall in general quota or be considered under the master's quota as well.

To qualify for Master's quota, you should have been awarded Master's degree by an accredited U.S. institute of higher education.

My wife is currently on F1-OPT status and it expires in June end. I am on H1B Visa and need to apply H4 visa for my wife.

I don't believe company attorney's will seek COS for your spouse at the company's costs. It does not hurt to ask though. If they don't cover the...

Am I eligible for cap gap extension?

I can understand the confusion. Cap-gap is granted to students to continue to stay in the U.S. to join their petitioning employer on Oct 1. Since...

Travelling out of country when H1b is filed

You can leave and return on H-4. COS will be considered abandoned and denied.

I am having a affair with a guy on Internet who is 15yrs younger then me and he lives outside the US, but i want to marry him.

You seem to have options - Fiance visa or immigrant visa petition

Can I apply for Opt ext and H1 at the same time with different employers?

I would not file multiple extensions for different status at the same time

I got a receipt number for my I539 application.

No

Applying for PERM in 6th year of H1B

Employee substitution is not permitted anymore.

The H-1B petition will most likely be rejected. Nunc pro tunc is for situations beyond your control. I don't see it helping your situation.

Working for US company from a foreign country

The question should be addressed to the company's attorney.