Have you checked for exhaust leaks?
While adding pipes and an open air filter, it will in fact cause a lean issue, but I'd imagine that being at your elevation, may make up for it a little, as the air is less dense, and the bike would run richer.
I'm a huge fan of the TTS system, but it will require the addition of bungs for the O2 sensors.
Dobeck makes a simple tuner that adds fuel in the idle, mid and top end ranges, that although isn't as accurate or precise as the TTS or other units, it's also not as expensive.
“When the going gets weird, the weird turn professional....” ~ Hunter S. Thompson~
R.I.P. Rubberdown. 1971-2012