Nlts and rev limiter settings

[chanley talon]

Hello i have a key driver chip with Nlts and adjustable rev limits. If i do not get the clutch wire hooked up right could it cause me to hit a rev limit, if the ecu doesn't know where the clutch is. In or out? Because my car is cutting out at 5500 rpm? This is a 5 spd car not my 1g auto, Thanks for any answers.