When I went to forward controls with my '06 FXDLI, I had the problem with the mid-control shaft too. I found a website that suggested rotating the shift linkage clockwise and pushing the shaft back through the primary until you can wedge the upper end of the linkage behind a bolt on the engine. The shaft ended up flush with the outer primary case. I covered the shaft end and opening in the primary with a piece of metallic foil tape cut to the size of a nickel. Later I bought a round HD emblem (about the size of a quarter) that stuck with an adhesive backing over the opening and shaft end. It has been there for a couple of years with no problem. Hope this helps.
