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The 2009 Matrix S shares the same 2.4L engine that is in the Camry and Scion xD and tC - might be able to repurpose one of those kits to suit that engine. That way you are not starting from scratch, buying a part that is already mass produced. Assuming this was the way your are heading, since you inquired about the tC ECM wiring pinout (slightly different, might be able to work around it once you find the pinouts for the 2009 Matrix S).
As for reflashing Toyota ECMs, not really viable. Toyota hasn't opened up their ECMs to tuners or allow for provisions to "reflash" the ECM in that manner. There are some parameters that can be updated with a Toyota scan tool, but not enough to account for a forced induction package.
Piggyback vs standalone depends on your power gains, budget, and future plans. Emanage units have had pretty decent success. Same with Camcom and others. Decent piggybacks that have enough forum support to help you out. For standalone, like an Apexi Power FC or AEM EMS or Hydra EMS system. Others have had good luck with Unichip Q and Megasquirt - lots of choices out there.
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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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