Am I allowed to drop a Proton Bomb while I have an ion token? I am moving as if I was assigned a maneuver, and not using my maneuver dial.

I'm pretty sure the answer is no.

If you are under the effects of the Ion rules, 1 token for small, 2 for Med ships, you don't actually reveal your dial, so the triger for dropping the bomb never goes off.

I would have to say you cant drop the bomb. When your ionized you don't assign or reveal your maneuver dial.

What Vanor said.

I think this one was actually FAQ'd, and is at least anecdotally part of the reason there is some question about whether Advanced Sensors works when you're ionized. Only I can't find the actual FAQ bit where they said that - maybe it was in a ruling given at GenCon that is going to be in the next update. Anyway I believe, for whatever it's worth, that it has been said from on high that you cannot drop a bomb or mine when you have an ion token, because you do not have a maneuver dial to reveal.

In this case, the ability's text is far more conditioning than Advanced Sensors.

It only works when YOU REVEAL a dial. Here, I have no problems to rule that if you don't have a dial, you can't perform the action on the bomb cards.

I think this one was actually FAQ'd

I thought so too. But I couldn't find it in the most recent FAQ either.

the only thing you can drop while ionized is a proximity mine