That is the current immigration law in the US.

This may be best to have an attorney review your case history.

An entire GC application is required in this situation.

It is not advisable to travel given information provided.

No the file will be transferred and cannot be refused. Wait for further correspondence with USCIS.

Yes this appears normal for USCIS.

Yes this is possible despite overstay. Consult with an attorney for guidance.

Yes you should still be able to enter with valid visa.

Yes you may contact USCIS re: your concerns.

For next best steps, best to consult with an attorney.