Tune ups, jetting, post-cold weather, etc.

If you already have the jets, try going a size smaller on the main and see how it runs after the engine is warmed up, if it's blubbering and 4 stroking then go down another size and repeat until the 4 stroking clears up and it revs clean.

If you got the pipe already, go ahead and install it since it'll give you a very noticeable increase in power, then after the p[ipe is installed take it for a ride and see how it does before playing with the jets.

You might need to get a soldering iron or a propane torch and some electronics solder and then get a micro drill bit set and pin vise then you can solder some of the jets you got shut and redrill them to get the size you need. These bits are number sized and the bigger the number the smaller the hole they will drill and most 66cc engines will be in tune with a jet drilled to #72 or 73, but at the higher altitude you live at you might need to try #74 or 75 before it'll clear up and run clean. You can get these microdrill sets from widgetsupply.com and the kit comes with bits sized from #60 down to #80 along with the pin vise to drill with, and the solder you can get from radio shack, harbor freight, or just about any auto parts store that also sells tools.

I agree with Dave, if you're going to run a pipe you might as well put it on, no use going through the whole process twice!
I have been trying to get my RT type carb jetted right, too. It seems that if it is jetted right at low to mid RPM, it is too rich at wide open.
I put a smaller jet in, picked up some top end speed but it seemed too lean at low speeds.
The spray bar has two holes, the higher (full throttle) hole being the biggest.

Since I still have a good NT laying around I decided to try some stuff on the spray bar. I took a number 11 exacto knife and twizzled the lower hole a little bigger. Sure enough, it richened up nice on the bottom. Next step would be to try one step leaner jetting, but-

During these experiments I developed a problem with the back tire going flat repeatedly which I've decided to blame on my bike's cheap, low pressure tires. (Genesis Onex, 29) I'm big and I think they are getting pinched or even rolled off the rims in corners due to the low pressure. It only started after they had 300 miles on them, I weigh 255. The miles (or my big white butt) might be softening up the sidewalls.

I have new Contis coming tomorrow with MTB tubes and liners, they can handle 58 PSI. I'm going to continue the carb work after the new tires are on there. Each time I got a flat I was the farthest from the house I usually go. I have a bad leg and 2 mile walks are a major problem.

Oops -
That RT carb stuff was a little deep for non-mechanics- it isn't necessary unless you get annoyed by little glitches, the carbs run just fine over 90% of the range.

The spray bar is the brass tube in the throat. It brings gas up from the main jet. It is in the center of the carb throat, the holes are the metering jets that are uncovered as the throttle slide is raised. They point toward the engine, the output side.
On mine it is slotted so it can be turned or removed, but I found it very tight and decided to leave it where it was.
If you are new to all this, just get it jetted as good as you can, maybe you won't even have any trouble, since you are at a higher altitude and will be running a pipe.