Sounds like you are comfortable enough with doing the work. Even though they don't necessarily advertise it, you can usually call Factory and they'll put together a "high altitude" kit. Sometimes it is just a matter running a little leaner on the needle and main jet. CV carbs actually do a pretty good job compensating for altitude to some extent so it should only be some fine tuning to make it work right.
If the bike isn't modified, I would start by figuring out why it isn't running clean under 5K. Think about it, you are at high altitude so you have less air and you are blaming it on a lean stock needle. It could just need a good carb clean and minor adjustments, it could be the nature of this bike at high altitudes, or it could be that you need a jet kit.