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I know it SAYS not to use them. It just doesn't feel like the tranny stops are very rigid, or are too far out. I can put the car into car and push the shifter much further that seems wanted.
I would recommend you do not use the shift stops with the short shifter, since the transmission has them built in there is no need to use them. Also it may be detrimental to the transmission as the transmission may not fully engage the gear and you may damage the transmission.
The simple question is, why would you use the shift stops with the shifter if your transmission has them already and the manufacturer of the transmission strongly recommends against using the ones with the shifter. Seems a no brainer to me.