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Sounds like you could be running excessively lean (too high an exhaust temp) or the timing is so far off you are dumping raw fuel out into the exhaust (late combustion).
Assuming you tried to swap in another ECM (one from the 2002 Toyota)? Was the donor Toyota engine known to be a running part? If the donor engine jumped a link in the timing chain or the original timing was goofed from a bad repair - that could explain the headaches that you are having now.
The 2000 Chevy Prism engine "should" be identical to the 2002 Toyota Corolla - though there are some electrical differences. I know that others here have used the later 1ZZ-FE engines to swap into their Prisms without too much issue.
Timing is controlled by the ECM, if that is not timed right (firing order is different than the Chevy ECM), you won't be able to fix it without replacing the ECM. I'd start off with the easy stuff - see if a sensor was left off, damaged or shorted wiring - especially from the crankshaft and camshaft position sensors.
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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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