Even in the UK (yes it does get stupidly hot here sometimes) my 05 gets hot, ive even seen it melting the grease in the head bearings! You can see the top seal weeping on a really hot day. I dont know the answer other than wire in a manual switch to the fan to keep the bike cooler in trafic.
I also have a 99 R1 and that was even worse than my 05 FJR in the traffic, but there is a mod and its as simple as replacing the fan sender switch for one out a Honda Accord (yea i know) but it drops the fan cut in from 105 deg to 91 deg so the bike stays so much cooler. The cooling fan is on a lot more but the bike is so much cooler - even the frame is noticeably cooler.
05 FJR Silver & Blue
19 plate MT10SP / crazy but i love it