You are correct about your secondary O2 sensor. If you install the TS bypass, your only options to avoid a CEL is to either have a new cat custom spliced into the system or install the later model headers with a cat incorporated into the header (not sure if this is direct on), or get a ROW flash which eliminates the need fo a second O2 sensor.
If you decided to drive it as is with a CEL, I'm not sure what that will do to your engine management system. It may go to factory set mixture settings utilizing throttle position and MAF to determine mixture.
Let us know which direction you go...
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