Buckfever - couple of thoughts here. First is that airlines do not treat your guns well and I have seen them just toss the case around - I rarely see one handled gently after it leaves the inspection desk, so I would go for the strongest case you can get and expect to resight your rifle after the trip. Second is to seal it with a color tape they don't have at the airport so if someone tries to get into the case you will see that your tape has been broken and you can call for assistance and make a report if necessary. Third - most security (including police) I've met at airpports while transporting my rifles give you the look of death - like they wish you could make their day and may well treat you like doit or pond skum, so expect harrassment and delays; and fourth - I think that if you pack ammo in the same bag or container you pack your rifles in you will probably go to jail - they like that stuff as separate as you can get it.
The transportation security people will probably check the case in your presence and ask you questions, etc. It is best to have the rifle disassembled - bolt out so they can look down the barrel and comment on its cleanliness (snort, snicker) - actually, the security people may not even remove it from the case to inspect it but just observe to see it is properly dismantled and ammunition is not stored with it.
Best to call them first for specific instructions.
Removing the padding - I think you can most likely find a two gun case without a problem and considering the bumps the case may well take you may wish to consider leaving the foam in the case. HTH. Mikey.