Your 09 had a cat? Was it a california or international bike. I thought the 2010 was when they started putting the cats on domestic bikes.

 

I have a 2013 Street Glide - stock other than Motofuel Jackpot mufflers and I added the Harley Davidson Burst breather. I noticed the right side of the motor getting very hot and it feels like the rear cylinder is shutting down at idle way sooner than it should on a ride. Does this sound like I am running lean and need to tune the bike?

 

If you've increased the air flow through the scoot, you'll need to add a fuel management system like a Dynojet or have it retuned. It'll run too way lean which means more heat. A richer mixture will cool it down somewhat.

 

EFI and a bad tune in my opinion has caused the air cooled V-Twins to run hotter.
A Mikuni Flat Slide Carb on any big inch V-Twin runs cooler because they use too much fuel and are not near as perfectly tuned as fuel injection.
That being said I'll take EFI and a great tune over a carb on my bagger and never look back.