What should I do at the time of tax filing? Should I include 1099K? What are the chances I will get a query?

yes you should report the information because you have to be truthful

Disadvantages of filling petition Form I-130?

It would be best if you could get into H-1B status because there is no issue of immigrant intent.

Can I submit forms I-130,I-485,I-765, G-325,I-864 all at the same time? Or Should I submit I-130 first and wait for the receipt?

You should submit all at the same time if possible.

From F1 to I130 or Adjustment of Status?

I agree - it would be best to wait until the girlfriend is a U.S. citizen.

How long it takes? Is it faster through lawyer or the same period of time if I make it my self

The only reason why it may be faster with a lawyer is because, if you mess up the application on your own, USCIS will issue a request for the...

Any issue at POE since duration in ds160 and current duration are different? Any risk of my sister being denied entry to US?

It is almost certain that what was mentioned on the DS-160 will not matter.

Do you think I should change start date in my contract to 08/12 and not leaving gap in status OR 09/01 OR keep it the as is?

If your attorney doesn't know what to do, maybe you should consider consulting with a new one.

I am a granted Asylee and a green card holder for couple years now.My parents were declined for visitor visa from Egypt.

It seems like it would be easiest for you to meet them in a third country.

L-1B and L-1A are nonimmigrant visas, I think you are talking about the EB1 green card which does not require a labor certification.

Can my son get any legal status if he came to the US in 2011? i dont have any legal status either

From the facts you presented there doesn't seem to be a basis for working.