Originally you said, "jutter", which by definition is a, "beachcomber"., well, here in California anyway. Then someone said, "judder", meaning, "to shake violently". Can you be more descriptive about what you are feeling/hearing and when you feel it. I am somewhat able to relate to the word, "shudder", which is in the dictionary and means, " to tremble with fear". You feel the bike tremble? I hate being so picky but words matter and all these guys who want to help you need to be sure they really understand what you are talking about before their expertise can be accurately applied to your issue.
So, what exactly is happening when you shift between gears? So far I don't have a clue other than guessing what you might be feeling and/or hearing.
I went back to see what I am missing and I see you said in one post, " ...a judder or faint clunk...". A "clunk" is something I can relate to. My 2006 Classic exhibits a very, very slight clunk sound when shifting from neutral to 1st, gear. Same thing when I shift up through the gears but I do not hear it, I feel that in the heel of my boot when up-shifting or down shifting but it is almost imperceptible. The most pronounced clunk I ever hear is when I am maneuvering the bike in my garage with me on the bike and it is running and I hear and feel a very slight clunking sound, helmet on or off, in the drive shaft in first gear. Do you wear a helmet? I do and at 75 my hearing isn't great so I don't hear much other than the wind and the music I get through my helmet speakers. Sorry to ramble on.