The only time that I have experienced any issues with sputtering is at high RPMs in the 7500k range and higher. The bike has never stalled while riding. But I have noticed at higher altitudes 10000 feet plus that it does buck unless I drop a gear and get the RPMs up. This also started about the same time as the Texas trip. Although what I have notice is very erratic and broad range of MPG. Until the trip to Texas I was consistently in the 43 to 48 MPG range. While on the way to Texas and back I had a very broad range, as much as 51 down to 30 MPG. Since trip it has been up and down but nothings with any consistency. Yes there were some high winds along the way but I have run into them before without the extremely change in MPG. Maybe as low as 39 with two up.
I'm no carb techie, but all those factoids sound to me like some fairly serious carb clean/rebuild may be in your future; I think 6000ft elevation is about where folks say you must get high altitude carb adj and/or different jets, so your Castle Rock location is right on the cusp...
I'd give the bike a couple good doses of SeaFoam, AND, I say, SeaFoam likes to SIT, i.e., just running a couple tanks (at approx one oz/gallon) doesn't seem that effective. I say put SeaFoam in, make sure it gets mixed around in the tank a bit, run the bike 5 minutes if possible to get the mix down into the jets, then let the bike sit for minimum 3 days, 4 - 5 being preferred. I think the molecular binding required by SeaFoam for deep cleaning (i.e., fine parts like jets) is probably a slow, difficult bind, hence the time requirement.