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Misfires can't jump from cylinder to cylinder in that manner - unless the original problem was a bad or intermittent coil that happened to be on the offending cylinder.
I would look into an electrical issue with the ECM, especially any electrical interference, poor chassis ground points, EMI from newly added electronics, etc. The 1ZZ-FE engine is pretty sensitive to electrical noise.
I wouldn't rule out a fuel or spark plug issue either. Pull the plugs out and read them - noting any changes. Drive normally, see if you get #2 to misfire and immediately shutdown the engine. Remove the plugs and re-read them to see what is going on (allow to cool first, of course).
250,000KM (~155K miles) is pretty decent number of miles, but I wouldn't consider that too many miles for this sort of engine. They recommend an audible check of the valves - normal adjustment is not needed in most cases. I've checked clearances on both my cars for grins - they have been spot on - have 165K miles on the Corolla and 115K miles on the Matrix.
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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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