I have an ST1300 and I have a similar problem with it. After riding many hours, my knees are just hurting from being in the same position for so long. There just doesn't seem to be any way of fitting some sort of highway pegs to it. I asked on the ST forum and was told to get a HD b/c this bike wasn't meant for that. Other than that (and no cruise control) I love my ST1300.
With the GW/F6B, the mick o pegs are available and I know people that swear by them.