VNN

I understand why you made your decision to delay.  
 
To be fair, “internet” people do not give wrong information: you can file AOS any time as long as marriage happens within 90 days because out of status is forgiven/not a concern for the application itself. They just do not highlight the fact for “what if” you encounter a law enforcement officer when you are out of status.
 

There has been always a risk associated with not adjusting the status in timely manner.  Many do not take it too seriously because the chance of getting caught is slim and you, unluckily, just happen to be in this slim chance.
 
To have a good sleep, many  people in VJ advise to file as soon as possible as you never know you can be in bad situation.

it is quite normal, to balance service centers' workload.

She does not have any option rather than come back to Cuba.  
 
I cannot comment on the relationship but it is important that you and your wife absolutely sure that there is no chance your marriage won’t work otherwise it will result in some deep regret in the future. 

DNA test (technically, it is not “required” but highly suggested). It can be costly due to the test itself and the shipping fees. The steps:
- Get a list of approved labs and choose one.
- Take your mother there to get her sample
- The lab will send the kit to your sister so your sister can get the her sample the she can send it back to the lab.
- Once both samples are analyzed, the result will be sent out.
 
I helped a friend on this topic long ago as her parents lost all of docs during the war. The key is to contact some labs and find one that is familiar with this process. It was like a decade ago so I forgot which one but I assume it should be easier to get DNA test nowadays. 
 
Your mother can continue collect other documents to support the case and submit anything she can have by the deadline.

You can put the newest one # or just leave it blank. Beneficiary’s passport won’t be really needed until NVC stage.

Write down Passport #2 since it's the most current passport with US entries at the time of filing. 
 
No passport copy needed for the I-130 beneficiary. Just write down the number. 

It may not be a big problem, however, he just needs to tell the truth by disclosing it “Yes”.

It may not be a big problem, however, he just needs to tell the truth by disclosing it “Yes”.

The only option you two have is to get married, then file I-130 via consulate process. No one wants be apart from his/her love one but again the option you have is limited. 
 
 
 

Your parents can.
 

4. What documents do you need to show that you are a lawful permanent resident?
If you are a lawful permanent resident, you must file your petition with a copy of the front and back of your Permanent Resident Card (Form I-551). If you have not yet received your card, submit copies of your passport biographic page and the page showing admission as a lawful permanent resident, or other evidence of permanent resident status issued by USCIS or the former INS

You do not need to do anything, it is automatically extended.

The only option you two have is to get married, then file I-130 via consulate process. No one wants be apart from his/her love one but again the option you have is limited. 
 
 
 

The only option you two have is to get married, then file I-130 via consulate process. No one wants be apart from his/her love one but again the option you have is limited. 
 
 
 

The only option you two have is to get married, then file I-130 via consulate process. No one wants be apart from his/her love one but again the option you have is limited. 
 
 
 

That what I did on my I-130.  I filed a I-129F before but I could not remember the day and month and I did not keep the receipt #. So I used the date of the check got clear.  Then I noted on Part 9 that was an estimate date as I could not remember extracly.
 

We did 1/2 page for each month of chat logs for CR-1. The primary purpose was to show the communication has been continuous.

- You must establish your residency and it must be established for certain period of time. You need to check this requirement. 
 
- Complicated divorce requires a (good) divorce lawyer. I tried to do a divorce paperwork before, even there was no contest and it was not easy .
 
- You are USC. Only US Government can revoke your USC but they must have a valid reason and prove that you lied to get your USC. The chance of deportation is like 0.000001% (I make this up but the point is do not worry).
 
Edited: You may consider to place some “.” and “,”. Very hard to follow your story.
 

No. You must apply Adjust of Status (AOS), however, you can also include Advance Parole request to be able to travel out of US while you AOS case is pending. It will still take like 4 months +.

No. You must apply Adjust of Status (AOS), however, you can also include Advance Parole request to be able to travel out of US while you AOS case is pending. It will still take like 4 months +.

They do it on on types of visa application (certain service center does certain types) and case by case basic.  It won't be an issue as the petition will most likely be approved before the PD becomes current.  In the case of non-immediate relative (Family Preference Immigrant Visa) , having I-130 approved very sooner in the process is not actually a good thing.
 

You can only include what you have.
 
Have you considered a joint-sponsor ? 

- You must establish your residency and it must be established for certain period of time. You need to check this requirement. 
 
- Complicated divorce requires a (good) divorce lawyer. I tried to do a divorce paperwork before, even there was no contest and it was not easy .
 
- You are USC. Only US Government can revoke your USC but they must have a valid reason and prove that you lied to get your USC. The chance of deportation is like 0.000001% (I make this up but the point is do not worry).
 
Edited: You may consider to place some “.” and “,”. Very hard to follow your story.
 

1. I mean... divorce doesn't really matter now. But the fact that you abandoned your residency (I understand you have been out of the US for more than a year now), moved to Pakistan and your green card already expired (so you missed RoC window by quite a lot).... I don't think your RoC has a chance to be approved, really.
 
2. I think right now having a lawyer is a MUST.  But personally I doubt even lawyer would help much.

Or you can also send submit your case inquiry and ask them to re-send the notice
https://egov.uscis.gov/e-Request/Intro.do
 
It will take awhile (3-4 weeks) until they re-send it.