Update: After removing the Power Commander 3 and the problem disappearing, it began to resurface 3 or 4 days later. I started keeping track of when this problem would occur and under what conditions. It took quite a while but suddenly one day I had an AHA moment. I knew the culprit. But to be sure I started predicting when it would occur and when it wouldn't. And I was right every time. It is a fuel pickup problem happening inside the gas tank. Only when I have 1/3 of a tank or less and as I come to a stop the remaining fuel is thrown forward to the front of the tank -- away from the fuel pump and its pickup -- and the injectors are starved of fuel and the engines dies. After coming to a complete stop the remaining fuel in the tank sloshes back and levels out and the pickup can get fuel again. The bike restarts easily, idles fine, and accelerates like a demon. Until I come to a stop again and the problem reoccurs. Fill the tank up and the problem completely disappears until it gets back to the 1/3 full level and it all starts over. Removing the PC3 fooled me because I filled the tank up at the same time making the problem disappear. I broke the cardinal rule of troubleshooting and made 2 changes at once.🙁. So then after taking it to the dealership to let them confirm and possibly fix the problem they discovered that the tank etching and lining process to remedy 5 years of storage with bad fuel left in the tank did not take and is already beginning to bubble and separate from the inside of the tank. The rust damage was just too great. Sooooo I've got to replace the tank. ☹️. I have located an '04 tank in pretty good shape for an excellent price (😉🙏 thanx Curt) and posted the question of fitment to my '05 and (🙏 thanx to Cogswell) he has assured me that the fitment will be the same.
As a side question, is there anyone here who has seen the inside of these tanks and can tell me whether or not there are baffles welded into the bottom and/or sides? That seems to me would prevent my problem from happening but maybe mine got rusted out during the 5 years of storage? As far as I can tell there is no way to change the height or level of the fuel pickup to fix the problem so I am hoping that just replacing the tank will solve my problem. If anyone knows different please inform me and have my gratitude for the education of a VFR dummy. 🤪