Employer owns two businesses at the same location. Company A applied for my H1b but he wants to pay me through Company B.

You are only authorized to work for company A.

What can I do ? Would they deny my application.

You don't know if there were any issues? Nothing came up during the interview? That kind of delay is out of the ordinary unless there's a reason...

What can I put down as explanation. Can I tell USCIS that my wife refused to sign my documents?

You need to at least consult with a lawyer before you respond to USCIS. If at all possible, hire one ASAP.

Can I apply for change of status within USA ?

Yes, makes sense. You should discuss in a consultation possible complications and processing times and whether it makes more sense to do it in the...

Am I legible to get a green card?, is there any penalty for being a F1 visa holder ( out of status )? .

No punishment, you can adjust status based on approved I-130 and the sooner the better. Talk to an attorney before you file, and I recommend you...

Can a person come here on a non-immigrant visa, but then do something X and get to stay here (immigrate) instead?

You should review the list of nonimmigrant visas to see what is available. You ruled out the more common ways, others include employment based...

My understanding is that you have 60 day grace period after post completion OPT unless you have accrued more than three months of unemployment. ...

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Border crossing between WA and Vancouver

They may have scanned your Greencard. Limit your stay out of US to six months in any case. You can check your entry and exit records online here...

Labor applied in 6th year, getting H1b Extn without PERM labor approval

You might want to take all your documents to an attorney and get a second opinion. Don't see basis for extension based on your email.

Boyfriend is awaiting citizenship thru army, plans to file me AOS after. Will there be problems if we get married soon?

timing of marriage could matter if you are traveling as F1. Sounds like a consultation with an attorney is needed so you can understand the...