Got a new (used) 2007 Street Glide the other day. It has V&H slip ons, but the stock air cleaner set up. Runs fine.

If I leave the pipes as is and add the SE air cleaner package, and get the stage one download, will there be any issues with popping on decel or backfiring?

Better performance? better sound?

 

Put your $$$ towards a PC-V and a new A/C.
Your bike will run much better and some what cooler as well.