No this is standard and nothing to be concerned about.

Contact USCIS to inquire about why the fee keeps getting rejected.

Use the newly assigned A number for case reference purposes.

No an extension is not necessary with pending AOS.

Yes this may impact your citizenship application but best to have an attorney review the criminal case to confirm.

Best to consult with an attorney to discuss options available.

No not automatically but may need to be explained with showing of timely submission.

Yes it depends on the case but generally reviews follow timings posted.

Refer to the USCIS webpage for a checklist. Consult with an attorney for guidance.

No not through sibling based petition unfortunately.