I did a commander-directed investigation and learned a LOT more about the process.
1. You have a right to talk to ANY IG within your chain of command: the base IG, NAF IG, MAJCOM IG, or AF IG. Local IGs indeed answer to the local commander and if you feel the local IG can't be impartial, you have a right to speak to any of the aforementioned IGs. If anyone impedes your access to an IG or even alludes to it, they can be prosecuted and the AF JAG Corps takes this one pretty seriously if it ever comes to trial; it can be a career ender.
2. You can also talk to your congressman/senator with the same level of impunity. Prosecution for violating this is worse than the above. If all 7 of you have different congressmen/senators, going to all of them en masse may be a viable tactic to get results.
3. It's possible criminal negligence may be involved here. I would HIGHLY recommend keeping your current commander in the loop and consider talking to JAG.
Fuckin' Two
Doesn't surprise me. They had a Captain get passed over for Major because someone didn't want to type up a PRF.