Thanks for all the response guys.
Let me "spin" something else into this equation.
I have one of those Alpha N digital fuel processors, the one from Gary Betherum at World Thunder Express. Gary installed it when he did my dyno tune. And even though he did a great tune, and got the bike to run better than before, it was not, I hate to say, "perfect". There was that occasional "pop" while shifting, a low idle when cold, and mpgs in the low 30s.
So I got the idea to check my TPS voltage. Using the SERT data mode, I checked and adjusted it per the instructions in HD Service Bulletin M-1101 dated April 25, 2000. The TPS read .38. I adjusted it to .61.
When I fired the bike up, it idled fast and high when cold, and then dropped down to about 950-1000rpms when warm. I rode the bike all day today, and not a single pop while shifting. I purchased gas and on the remaining fuel I had used, I averaged 35mpg, so the fuel economy is coming up too. I think/hope I resolved my outstanding issues. I just need to see better fuel economy to really know.
Here is my hypothesis (Wild Ass Guess) on what happened. The bike was dyno tuned with the TSP in a lean setting. The lean setting was across the board. This lead to the low idle when cold, and the occasional pop when shifting. The O2 digital fuel processor read the lean condition, and made up for it by making the ECM add more fuel across the board. When it was unable to accomodate rapid changes, like during a fast shift, sometimes the exhaust pop occured. This overall enrichening lead to poor fuel economy. By adjusting the TPS, the fuel processor now reads proper burn, and minimizes fuel usage. And it no longer pops.
What do you guys think, plausible?