You should file the I-485J with USCIS to avoid any issues.

You would need to coordinate with the warden of the jail. You could apply for a tourist visa to do this.

If you are not in removal proceedings, you can simply leave the U.S.

Definitely not recommended. Get a stamp in your passport instead.

You can file a FOIA lawsuit to correct the records if in fact the record is incorrect. If the record is correct, you cannot change it. An arrest,...

If CIS does not put you in removal proceedings, then you cannot go to the immigration court. You do have to exhaust your administrative process...

No, one does not include one's ITIN number anywhere on the H4 application.

The only rule is the rule of thumb, which is that you should wait for six months.

The I-485 date should control when to expect your initial processing.

You have not had an H1b in the last six years so you are subject to the numerical cap, it seems to me. Certainly you cannot port to a new employer...