Mine does it at slow speeds. It's always the 1-2 shift. Thought it was me at first.
That transmission take apart sounds like a real nightmare. It is possible changing the shifter could allow them to void the warranty. They can blame the situation on the shifter and get away with not repairing your transmission.
What I might do is put my stock shifter handle on before I take it in the dealer. The Barton lets you have either.