Running shoes (my feet hurt!)

I have been running for about 2 years off and on, but have only begun putting in longer runs (10+ miles) since March of this year. So pardon me if this question is ridiculous.

I went to my local running store and got fitted for some shoes. And let me tell you, they're great. I had been just running in whatever I found that was on sale, but to spend a little extra and get the right shoes was definitely a good idea.

This is my problem. The bottoms of my feet really, really hurt when I am on my long runs (10 plus miles). Normally they feel better the next day, but during the run each step is just misery after certain mileage. I have put over 100 miles in these shoes so I'm certain they don't need "broken in". I also bought some orthotics (just cheap ones from Wal-Mart) and they do seem to help some, but I'm still in some pain. Short runs don't bother me at all. And it's the entire foot that hurts.

My question is, do you just get used to this whole hurting feet thing? Is the pain just a result of increasing mileage, and therefore something my body will adjust to after time? Or do you think I need to suck it up and get new shoes again? And in case anyone asks, I typically do my short runs on a cement trail behind our apartment but for longer runs I run on crushed limestone or asphalt.