I've traveled with both long guns and handguns over many years. I've never had a problem although my one basic fear was that at either the departing or arriving airport, I would be asked by the authorities to prove that I can have, in my possession at that location a firearm. The would mean having a permit for that state. Not once, however, in all the trips I've taken both nationally AND internationally (Canada hunting) was I EVER asked for an ID. You collect you bag/rifle case like any other piece of luggage and walk away. I've gone to Knob Creek, for instance, and bought off the shoulder of another fella an M1a which I simply put into a $9 rifle case I bought at K-Mart there and took it home as baggage, no problems at all. No one cares. The only place I believe you would have a problem is in NY. Even Boston, I've been told, doesn't check for permits. So, leaving from Logan (me a CT resident) should not cause an issue when checking my luggage at the ticket counter even though I don't have a MASS permit. I have NOT attempted this, however. I'm still of the mind that I should have a permit for the departing airport state at least although I'm told many times it's not an issue.
NOTA BENE!: If your plane is diverted to JFK due to weather and your flight is terminated there, STOP! You should NOT collect your bags containing firearms but contact a senior agent or manager and arrange for them to hold your bag until the new flight is arranged for. In NY you should NOT take possession of your bag/case because there you will be mishandled by the authorities for NOT having a NY permit (which is impossible to get). If they control your bags, however, you should be fine until you get home.
I have also shipped shotguns ahead of me when I was going to the Dakotas and the flight had to make multiple stops. Rather than take a chance on losing them I used UPS to my guides home and collected them when I arrived. (There is nothing more strenuous than having a bag with a firearm going missing! USA has lost them on me......twice......but I got them back within 24 hours but only after threatening USAir with the ATF which I had on speed dial. )
So, It would be my advice that you simply check your luggage as normal. You are fine with a pre-ban so be confident enough that you'll not have any issues collecting your luggage just as I haven't had any issues.
Rome