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What code is the CEL associated with?
Also, for the people that are still having problems with the swap:
Are you guys using the stock Yaris gasket (the black O-ring with the "tail" and the partial mesh screen) with the 1ZZ TB?
If not...you should use at least the "tail" portion. The slot that the "tail" fits in on the intake manifold offers a totally open channel through which air will get in and cause idle speed "hunting" and CEL's. The channel is large enough to suck in any partially set gasket maker and give you problems such as rough idle and CEL's.
When I did the install I cut off the "tail" from the gasket and installed it in the channel in the intake manifold with gasket maker. Once set, the "tail" creates a nice solid plug for that channel, and I haven't had a single CEL since I made the chip swap....not ONE!
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