So here's the deal. I have a 2014 FXDB with thunderheaders, screamin eagle stage 1 intake and fuel Moto efi micro tuner. I have been running this setup for almost a year with no problems other than decel popping. I was on my way from the east to west coast on a month long trip when my bike started sputtering. It did it just a little bit after I filled up on gas but didn't do it again for quite a few miles. When it did happen again it was bad. It's idling higher than normal and sputters while idling. When I turn the throttle it almost dies and just keeps sputtering.

I took it to the nearest Harley dealer and they said it was my fuel tuner that had went bad.

My question is does this sound like a bad fuel tuner? They want to sell me one or dyno tune it and their prices are crazy high.

 

My first call would have been to Fuel Moto. Not the dealer- were you surprised they tried to sell you something?
I would also try pulling the tuner and see if the problem goes away. A few miles without it won't hurt the bike.
You may have picked up some water in the gas. Drain the tank, add some Seafoam for the next couple of fillups.