3 touring bikes, all had shift linkage issues.
When I first got a Harley with a heel shifter, I tried it, and found it to be counter-intuitive to what I was used to. So I got to thinking about it. In an emergency situation, choices are probably the last thing you want to contend with...and I believed I'd be better off just intuitively knowing that the thing that changed gears was something I always used with my toe, and the only choice I had was up or down. I was not concerned about the wear on my boot...generally, I consider my footwear to be disposable, much like brake pads...if they wear out, I just go get new ones. In over forty years of riding, I've never worn out a boot due to shifting. If I did, and I felt I was married to those boots, it's a simple matter of having a shoe repairperson put a patch over it.
So, with those things in mind, I eliminated the heel shifter, and haven't looked back. When talking to and advising new riders with the same issue of 'do I keep it or does it go?', I review the same issues, and so far, everybody has considered what I've pointed out and within a week or three, eliminated the heel shifter.
I think there's a great deal of validity in the suspicion that the heel shifter could be causing the OP's problem...I believe that the heel is capable of delivering a lot more power to the mechanism...that said, if what we're talking about is the shift rod between the tranny arm and the shift arm up front, it's a pretty easy deal to get a couple of Heim joints from say, McMaster Carr, and a quarter inch rod, cut to size and thread both ends, and that will take care of the problem for quite some time, maybe permanently. Quite a few folks on this forum have done the same thing and report excellent results. In my case, I just replaced the cheesy chrome shift rod the PO had installed with the stock cadmium plated stock part, works fine for me. Some picky folks would tell you that the Heim joints are noticeably better, maybe so, but my needs and wants are simple. I probably wouldn't notice the difference, but if the stock part ever wears out, I think I'll heed my own advice and install Heim joints too!
The next item to FAIL will be the ball joints at both ends of rod between the front lever shaft and the transmission lever. Converting to Heim joints seems to eliminate that failure AND improve shifting feel. You can either get a high dollar custom shift rod or get Heim rod ends which will thread onto the factory rod. Additional bolts, washers, and a nut will be required to complete the installation.
This AND stop kicking it so hard! Mine is an 11 NO problem yet (knocking on wood)
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