I just did two things to my Sportster. I adjusted the throttle, and installed Vance & Hines Super Q Quiet Baffles.
The baffles sound great, exactly what I wanted. However, the bike is now sputtering and popping.
No stalls, but I felt like it might. What is the likely cause of this? How do I fix it?
The pipes are Vance & Hines Shortshot Staggered, and I removed the stock baffles.
It also has a Screaming Eagle filter.

 

So I let my exhaust cool down to put the heat shields back on.
After I started it again and it was much smoother, a pop or two but mostly smooth.
What is going on? Did the ECU do an adjustment?
I haven't ruled out a good-hearted gremlin.

 

The ECU may have compensated for the extra lean condition you have because of the intake and exhaust. If you really want to get it dialed in you have to get a tuner.

 

Thanks @nevil I'm good with it's performance for now.

 

My main concern wouldn't be with the performance, but the fact that the motor is running very lean and therefore hotter.

 

Wouldn't the baffle make it run less lean?

 

The baffle may create a little more reversion but will not affect the air to fuel ratio in a significant way. Once the exhaust leaves the motor the AFR is already determined.

 

Here's a mov of my bike. Does it sound like it should? I'm new to bikes, so I'm not sure.