My buddy (lefty29er) just installed a strup header last weekend. I seen he had the cel eliminator on the header, so we pulled out the instruction manual that it came with and it said specifically to install it on the header. I'm not saying it's right or wrong or if thats even related to your issue but just thought I would add that.

 

Installing a CEL eliminator on the header (AFR sensor) is wrong even if God told you to do it. By spacing the AFR sensor further from the exhaust gasses you're making it read lean, which in turn will cause your engine to run too rich.

The CEL eliminator goes on the secondary O2 sensor in the S-pipe after the header. It works by making the sensor read a leaner AFR which is how it would be if you still had the primary cat burning off fuel that wasn't burnt during the internal combustion process.

To the OP:

As Trevor suggested, find out what the code is first. If it's a P0420, try rotating the CEL eliminator so that it faces away from the direction of gas flow. This worked for me and I haven't had that code in 2 years now. Also, the TCS and VSC systems are both turned off when you have a CEL so that is why you've lost traction recently. GL

 

Well, the logic is the Eliminator spaces the O2 Sensor away from the gas stream thereby reducing it's sensitivity to oxygen in the gases. With the pre-CAT removed, the gases are essentially the same between the first and second sensors and the ECU would call foul. If the first sensor is running less sensitive than the second, I would expect the ECU would again call foul since there is no way the second O2 Sensor should detect significantly more O2 than the first. My best guess here would be the ECU has a lot of tolerance for relative decline in sensor sensitivity. However, there's another concern with installing the Eliminator in the first bung. That sensor is the wide-band and it's important for it to provide accurate feedback to the ECU in order to maintain correct AFR. Using the Eliminator there will reduce it's accuracy as well as sensitivity (Ah! I see Fred has already responded to this in the post above .)