qualified for I-485 filing even our marriage date was later than my
I-140 approval date but still during my I-485 pending period (before my I-485 approval date)?
Yes, She's qualified to file I-485 as your spouse as long as your I-485 is still pending (before being appoved).
2) If she is qualified to file I-485 as my spouse, is she qualified
for apply the EAD I-765 and AP while her I-485 is pending?
Yes, she can apply for I485, EAD and AP together.
3) What the difference for my wife's I-485 application between the
following senarios: 1) if I were a Green Card hoder; 2) If I am still
waiting for the I-485 (my I-485 is pending) ?
Usually it's faster for her to get green card if she applies during your I485 pending period than after you get your green card.
心動不如行動, 盡快開始申請吧. Good luck to you!