Motorcycle Repair: 2002 FLHRSEI muffler switch out, air fuel ratio, dynojet power commander

Question
Bought this bike in Denver and rode back to SoCal. Ran pretty well on the trip but at RPM <2000, she runs very, very ruff, almost sounds like it's had a cam added but I've been told not so.  Also popping off on deceleration.  So, do I need to have the bike remapped to accommodate the lower sea level.  I would like to 86 the SE mufflers and add better breathing and a deep throated sounding slip on (not the cracking loud sounding pipes).  Any recommendations and should I consider switching out the SE air cleaner for more flow and looking for a recommendation there as well.  Thanking you in advance for your reply.

Answer
WhatYou need to get the bike to run right is a Dynojet Power Commander 3 usb.  the Harley race tuner kit will just not do it. And is a wast of good money. If it were me I would install a set Of White brothers E-Series 2 into 1 exhaust system and this will give the bike about 10 horse power and 15 ft lbs of torque more across the entire power band and they sound great and look great and are made very well. top that off with the power commander 3 USB and a dyno tune on a dynojet 250 Load controller dyno with the air fuel ratio montor and you bike will run better then you could ever think. Change out the primary gear ratio to the screaming beagle 21 tooth primary gear and chain and then you will know what a good running Harley is all about. You do not need to change out the screaming beagle air filter kit. It will work O.K. for you combo. When you are ready to step it up a level after this let me know and we can go from there. You can thank me later.  Johnny 602-705-7474