Justin09

It will not be rejected when it is accompanied by an ITIN application (W7). The ITIN will be processed first. Then it will be added to the return before the return gets processed. You can go to a IRS Taxpayer Assistance  Center (TAC) and get her  passport certified for free or to an approved private acceptance agent.
 
 
1. A K1 is only eligible for a SSN if you go to a SSA office within the first 76 days after her entry. The window is closed now until she gets her EAD or greencard.
 
2. You can do that and have until October 15 to wait on the SSN. With a SSN she can get the $1400 third economic impact credit. With an ITIN she is not eligible.
 
3. You may file MFS and she files nothing, if you don’t mind paying more in taxes.
You can read why I think you will save with MFJ in another post I made https://www.visajourney.com/forums/topic/779952-tax-filing-question-aos-from-k1/?do=findComment&comment=10636148
 
 

1.  You MUST have a SSN or ITIN to file a joint return.
2.  You apply for an ITIN along with your tax forms when you file.  
 
https://www.irs.gov/individuals/how-do-i-apply-for-an-itin

Yes, #3 should be "0" if this I-864 is for your spouse.  That section is for people NOT included as the beneficiary in this I-864.. 
The result in #8 will still be "2"

Yeah, it makes no sense asking for it after passing all the requirements for the visa. Thank you though. 

Different government independent of the visa process simply trying to stick their nose in.

IRS Filing

I didn't.   The USA has no such document. CFO should know this.
 
FYI.  This is better asked in the Philippines regional forum 

You and about 4,000 others going through Manila are in the same place.   An email (which you have done) is all you can do to advise them you are still wanting to continue.  The consulate will extend the validity of the petition at the window on the day of the interview.