Working remotely from another country as a regular, non freelancer, employee

Doesnt matter for Federal Income Taxes, Only State Income Taxes. You will have to report the income in the State where you generate the income and reside. So report the income in California. But, If you do conduct business in Montana then you would have to complete a Non-Resident Tax Return.

I presume you mean "controlled foreign corporation" regulations. Many different countries have their own CFC regulations including Australia, the USA, etc. These laws essentially create a situation where the company needs to abide by the rules of multiple jurisdictions, and not just the one of incorporation. These regulations often stipulate that the "offshore" corporation may be taxed under certain situations (for Americans, an example of this would be Subpart F income) I.e. If an American sets up a company in Great Britain (or China, or Uzbekistan) and owns 100% of the shares, this would be classified by the IRS as a CFC. For Americans CFC regulations come into play when over 50% interest in a foreign corporation is owned by American taxpayers. If, however, you have over 10% interest in a foreign corporation, you should get proper tax advise and file form 5471 - Information Return of U.S. Persons With Respect to Certain Foreign Corporations. Other forms Americans may need to file include TDF 90-22.1 and form 8938. This above answer is a very broad overview, based on my own research and experience owning CFC's, it is not tax advise, and should not be used to avoid taxes.

Same as any other entity (or person). Entity pays taxes in it's domicile jurisdiction. Best you talk with a tax preparer in your home country to ensure you have all the details. And... If you're a US citizen + your SAAS company is generating massive cash, likely best to organize your entity in a low tax jurisdiction, like Bermuda which is home to Google, Intel, Verizon, etc. And... best wait till Trump's new tax bill passes. If he has his way, corporate taxes may drop to a point low enough to keep your business in the US.

The income should be reported by the individual or business that provided the service and earned the income. If the 1099 is in your name, you could ask the issuing Company to change to the S-Corp if that is who earned the income. In the future, have a written agreement between your S-Corp and the Company you are providing service. Also, provide them with a Form W9, so they know where to report the 1099 income at year end.

First I'm lot a tax attorney or even know anything about Malaysian tax law. I'm however a person that has moved around a lot and have encounter this situation before. You will must likely have to declare your US income in your home country. However some local tax laws allow for a deduction of foreign tax paid at source. I have not found a US tax treaty between US and Malysia but you should contact a local tax attorney or the tax agency there and ask if they allow deductions or exemptions for foreign tax paid at source. If they do, you would declare your income and deduct the amount of tax already paid to the US. You may or may not still be liable for additional tax on that income. Again it depends on local tax rates and policies. It's never a good idea to hide income from your tax agency though.