Citizenship - 5yrs continuous residency requirement in USA for naturalization!!

From you facts you appear to meet physical presence and resident requirements

What is the process now that my wife'svisa was approved?

With visa and valid passport she arrives in the US and resident card is subsequently issued

Divorced in the US but marriage not annulled in the Philippines?

Yes you marry since you are divorced in the US.

Can I adjust status if...?

It is likely you are eligible to adjust since your last admittance to the US is parole. See an immigration attorney for a full review

Premium processing is available for some visa classification. For visa classification and fee see USCIS.gov

How long approved H1B approved petition is valid for further extension?

Contact your new employer's immigration attorney that is handling the new H-1B and bring this information and question to the attorney.

How to obtain legal residence after a missed deportation order?

Contact an immigration attorney and a criminal defense attorney.

Should I have EAD( employment authorization document ) form I-766 for approved H1B status ?

There is no EAD for approved H-1B status. the approval notice with the I-94 is evidence of employment eligibility with the H-1B petitioning...

My I-90 application is pending, my green card expired Aug 11, 2017, the USCIS Processing Time Information is Sept 2016?

You will need to wait. Within a month or so of expiration try an info pass appointment seeking a temporary extension

Do I need to act on my spouse's i-539 which is in pending review even after stamping completion?

The application for an extension should be denied, however, USCIS does not always correctly adjudicate the application. Consider notifying USCIS of...