I have the flat black monster knob and a TWM Shortshift kit with base and cable bushings. I have had it installed for almost 2 years now and I like it. No more burning a shift pattern into your palms in the summer anymore. Its been quite a while since i have used a stock knob, but I would say I do like the setup overall. I have been itching for a new knob lately just for something "new"
Monster Knob vs Stock on top of my beautiful garbage can...
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I guess I could answer your question. No the "lower sitting" knob does NOT adversely affect your shifting capabilities.