I say uninstall the whole kit and re-install that way you know everything is connected correctly and go from there.
I have installed 2 different kits and haven't had that problem
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1992 SE-R w/GTi-R swap *sold*
1996 Infiniti G20t *sold*
2003 Nissan 350Z w/TT kit *sold*
2008 Infiniti G35s 6spd *sold*
2011 Subaru STi *Daily Driver*