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Some modules have their own diagnostic connector but those are usually high end audio modules found euro cars. Every module in this car will communicate through the dlc obd ii connector but I could be wrong. I would suggest contacting a Suba shop or dealer tell them what u did and ask to pull all codes or talk to the shop foreman. Keep in mind that if u left connectors unplugged because a component is no longer in ur car u could have opened a circuit unrelated to that component. Also ur a/c system communicates with ur pcm like turning rad fans on when ac is on turning ac clutch off when wot etc. my guess is u opened a circuit unknowingly or u pissed off a module do to a communication issue
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