I ran my swap with only one cat until recently. With only one cat i was getting a code but it was not effecting the way it ran at all. After i put in the second cat it ran exactly the samemwith no check engine light, the only difference is i lost a lot of top end power wen i put it in. I found a company online that makes a device u plug in instead of the 2nd o2 and it sends the correct signal to the ecu so it thinks it has a cat and the o2 is working properly. Once i get my truck refered and smog the cats are comming out and that device is going in.
Just my 2 cents. 
What is the company that makes that?
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