I ride an 07 Lowrider with a full Rinehart exhaust, PC3, and Screaming Eagle air filter. The previous owner added all of that and it runs perfectly. After 2 years now I'm tired of riding a loud bike. I'm thinking about going back to stock configuration. My questions are what stock exhaust will fit my bike (TC96 and original foot pegs) and will I have to retune/remove the PC3 with stock air filter and exhaust?

 

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The stock exhaust for your bike is also the same as for the Super Glide, Street Bob and Wide Glide (but only 07-09). So it should be pretty easy to find a stock take off system. You don't have to remove the intake and PC3, but you may need a new map for it.
You'll also need a couple of mounting clamps and the lower bracket.

 

Any 06-13 Dyna exhaust should be intrechangable, if you go back to stock AC and remove PC3 your EFI should adjust, I have a full stock exhaust from 2011 Street Bob minus the sensors, PM if you're interested.