The baratron is built into the ECM and should accommodate the pressure change - I've had my Daytona up to 10,000 ft and still runs well
There should be a hose from the ECM baratron to the airbox - make sure that hose is not kinked or folded. Doesn't make whole lot of difference if cracked as is really just sensing atmospheric pressure and airbox pressure not significantly different.
So you are obviously 'lean' at the bottom end - which means not enough gas for the volume of air. K&N would actually make situation slightly worse.
Try loading one of the TORS tunes with TuneECU, which will enrich things a bit for you.