What can I do to fix this situation since I don't wanna have any problems with the immigration department of USA?

There are lot of specific questions. Please set up a private consult with an Immigration attorney. These questions are not best addressed in a...

After how long can I apply for my green card?

Talk to an immigration about potential 1 step adjustment for the green card.

What should I do if my spouse wants a divorce and I have a conditional green card

Sorry to hear of your situation. You may still be able to file a I751 with a waiver. Talk to an immigration attorney and seek assistance. Conduct...

How do I go about this situation?

Please talk to a family law attorney.

An immigration attorney would need to review the I9. I suggest consulting with a qualified immigration attorney.

We were wondering she can continue being in the country past 2/4 even if we have not got the received confirmation from USCIS.

You should address the question with your employers immigration attorney. That said if the COS was timely filed it should be fine.

Can i apply a transfer through company B when the company A's extension is in process or got rejected and can i stay in US?

Please seek independent counsel from a qualified immigration attorney.

Is it a good time to apply for naturalization?

She should consider naturalization. She could opt out of the move from f2b to f1.

What is the best thing to do? Get a lawyer? Just turn himself in?

Please have him consult an immigration and criminal lawyer.

Does the K3 visa option work for Canadians? Does it shorten the separation time?

I would set up a consultation with a qualified attorney in your area.