The problem is that your dealer probably loaded the stage I flash and it's not a good map for your setup. e.g. HD does not sell Samsons and therefore would not have an exact map for the backpressure. You need some sort of a "tuneable" ECM to fine tune your bike. Some use the SE race tuner, some use a Power Commander, and there are others. I used a Power Commander with the SE Stage I air cleaner and a set of Rush slip-ons with the 2 1/2" baffles. PC had a map on file and the unit arrived pre-loaded with that map. Have not had any problems.
Does your dealer have a dyno? If they're tuning it without a dyno, you're just pissing good money after bad.
At this point, you WILL need some sort of tuner.
What you have to ask yourself is "do I trust my dealer"?
Find a performance dyno place and ask them for advice. That's what I did on my '06 Road King, and they were exactly right.
Nothing worse than having to pay twice and it still isn't right.