I also come to the FJR from a K12LT - perhaps that is why we think there is heat - but most folks on this board think there isn't. I find the heat on my left calf. This weekend it was 94 and I rode in Joe Rocket mesh pants with shorts under. It was DEFINITELY warm. I will probably NOT ride with this configuration of clothes again - at least not in the summer (when it is the only time I will wear the JR mesh pants).
I also feel a vibration in the higher rpms - mine is above 5k, though.
I have a low speed surge - and think that TBS will probably help. I have checked the TPS and it is good - smooth increments all the way to 100+ (mine goes down to 16 or 17 and steps up without skipping).
None of my vibration is enough to cause mirrors to blur - but above 5k.... I'm usually not worry too much about what is behind me as much as what is rapidly approaching.
Two up - my wife demands a back rest, too. Will probably go with the GIVI e46 when a bracket is ready. She said the seat is painful - I didn't tell her she was being a sissy as she also said that it would be OK to go for the custom seat.
I always thought the LT was about perfect out of the box. Certainly from the comfort side - I only changed the seat and the original seat wasn't bad. the headlights sucked, but that was fixed with PIAA 910's.
I am also very pleased with the bike. smooth and relatively comfy - but needs new grips and I could go with lower foot pegs and higher handlebars (or further back ones).
I'm not as partial to the windshield as I think except for the full down position that it is way too noisy.
mine whistled like construction crew on break. but this was easily fixed.
shifting is smooth once the timing was figured ot.