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I recently replaced the head gaskets on my winter beater. I also put a set of reman heads on at the same time because I was in a hurry and didn't want to wait for my heads to be resurfaced. I also took the time to "fix" some problems with the smog equipment and I wanted to know if it will cause problems. Here's what I did...
Smog pump was siezed so I removed it along with all tubing and had the machne shop block off the ports in the head. (I kept everything I took off just in case...) I also plugged the vacuum lines.
The EGR tube was broke so I plugged both ends. I reconnected the wires to the egr switch.
The truck is a winter beater and sometimes used to haul things and is driven less then 5k miles a year so it's emissions exempt. Also the only glaring problem is the missing smog pump, but I've had trucks pass with missing pumps before... (Names withheld to protect the guilty )
Im not sure how your computer will react to all of it though, I work on mostly carbed trucks. you could have some problems if it gives your computer fits that throw it into a closed loop mode