You can file NIW I-140 along with I-485 if you are qualified for NIW, and if visa numbers remain current after next week.
As for the rest of your questions: Let me ask you, is the I-613 you received addressed to you at the top of the letter, or is it addressed to the director of the USCIS service center?
If it is to the director, I strongly suggest that you write a clear letter to that same director at that same address, along with a copy of any and all case-related receipt notices/responses from USCIS and DOS (keeping a copy of the I-613 at the top of the pile) explaining your situation and asking them to reopen your case in order for it to be adjudicated.