When I was struggling with a pop after installing new pipes, a PCIII and getting a John Golden tune on my SED, he sent me a tip about how to install and properly torque exhaust gaskets and this quickly solved the problem. This might not be your issue, but if you try everything else without success, this might be the problem.
So you're gonna' keep the tip all to yourself?

To the original poster...if all they did was put slip on mufflers, they shouldn't have messed with the header pipe. But, it wouldn't hurt to take a 1/2" open end wrench (you might have to find an old one and cut it in half to have room) and check the nuts on either side of the exhaust flange on both pipes where they come out of the heads. Or get the dealer to check it. The coughing/sputtering...something ain't right.
Sledge...not discounting what you're saying about the backpressure thing, but there are a lot of mufflers that are "straight thru"...actually, it's the baffle that is straight thru, but I digress...that don't backfire or sputter when the bike is tuned right. The Fullsac system would be one prime example. A little tiny bit of backfire on occasion would not be as much of a concern to me as the sputtering/coughing.