What airline are you flying? TSA has basic regs for flying with guns but airlines also set there own rules aswell, so before I can be of real help I would need to know this.
TSA's Regs are here http://www.tsa.gov/travelers/airtrav...rial_1666.shtm
I fly with guns at least twice a year, only problems I have ever had was from lack of consistent training on TSA's part. So I print out the above page and keep it with me along with a printout of the airlines rules. I also call the locale TSA office and the airlines office and make sure that there hasn't been any last minute rule changes that haven't made it to the website yet.
You shouldn't need any extra time at the check-in counter (though I have no experience in your airport), all you have to do extra is tell them your traveling with a gun and then you will have to sign a paper stating that the gun is unloaded.
Last time I flew with guns I stuffed a Saiga 308, a Romainian AK-74 and an AR-15 into the same long gun case and I had 2 of my carry pieces in a lock box in my luggage plus ammo for all five...needless to say, the lady at the check in counter was :what:, LOL!