When I bought my '04 Gt last December, I decided ahead of time to have the ECU replaced before I even rode the bike. My thought was that it is better to have and not need, than to need and not have. After I rode my bike for about 100 miles, I took it back and told the dealer I was not happy with the performance and wanted the ECU replaced. I did have some minor hesitation which I probably would not have noticed if I had not read the bulletins, so it was a no brainer for me. I also put on a staintune exhaust at that time and have had no problems. I've got about 6500 miles on the bike.
If there is a protential problem with the ECU and you can get it replaced, I'd say get it done. You might need to approach the dealer with a strong conviction that you need it done, or they may give you some resistance.