I have owned 3 ST1300,s, 03 ABS, 05 standard, and 08 ABS. The 03 was hotter on my lower legs than my 93 ST1100ABS, but not that big of a problem. My 05 on the other hand, was very hot, to the point of being a distraction on trips, again on my lower legs. I did several mods, including removing the inner cowls, having the headers ceramic coated and then adding insulation wrap over the ceramic coated pipes, and it was better, but still a distraction.
Finally, after reading feedback from this forum on those that did a throttle body sync, I had my very talented Honda tech do that on my 05. It made a considerable difference and I was happy. Two other ST1300 owners also had theirs set by this same tech. The one that had the most severe heat problem was found to be out by quite a bit, mine was out less than his. The other who said his wasn't that much of a problem, was found to be almost perfect.
Now I have one of the rare 08 ABS ST1300's and I find it to be very comfortable as is. That perception was reinforced recently when I rode a used 04 standard that our dealer took in on trade. I couldn't beleive how hot it was on my lower legs, especially the left leg.
I have read that the 08's have a different part number for the ECU, but haven't been able to prove that yet, as the 08 fiche wasn't on line on Honda's site the last time I checked. If it is different, it could be that the new ECU plus the new shields behind the foot peg area help a lot. I may have the throttle bodies checked just for curiosity when I have major service done on the 08. I know for sure that my stock 08 ABS is the best of the 3 I have owned when it comes to heat.
I do know another thing for sure and that is there is a difference in one ST1300 and another when it comes to heat and throttle body sync made a difference in the hottest of the 3 I have owned.