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It depends on what exactly was swapped, engine wise - was the whole engine, wiring, sensors, and ECM swapped - just retained the manifold for clearance? Or did you swap in just the block portion of the 2005 onto the rest of the 2001 engine? The two manifolds are almsot identical, except for some bending and moving around you'll have to do to make it fit (this can apply to almost any header). Big difference is that the 2005 exhaust manifold holds an AFR sensor, not a typical O2 sensor. If the whole engine/ECM was swapped - this will cause a CEL to come on all the time. If just the shortblock was swapped (original ECM was retained, all original sensors, and exhaust manifold) - then you may not see a CEL at all.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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