Could it be the adjustment that's making it hard to up-shift? In-other-words, was that linkage readjusted when the heal/to shifter was installed?, thereby needing readjustment(back to stock positions) upon removal of the heal/toe shifter. As well as possibly other components.
I'm not real clear on if there's floor-boards or foot-pegs involved.. I might have missed that.. but thought I'd just throw this thought out. Good luck with it.
Possibly, but for clarification; I'm using what appears to be factory pegs.
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SFC, U.S. Army (Retired)