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VSC code, check engine lite, AFS (lighting tracking code?) on together.

(2006 Lexus GS300)
in Dousman, WI on July 08, 2013
On going issue. dealer said Y-pipe was cracked, expensive repair. He also said the engine misfired(cylinders#2 and #4), which has not happened again, so can not replace the engine until it duplicates. My mechanic (not the dealer) replaced all oxygen sensors(2 were also replaced in 05') and welded a small crack in pipe. Codes were gone for 2 days-now VSC and check engine light on again-noticed on a road trip that my gas milage has lessened. emission test this Aug. Not sure what to do--catalyic converter? Throwing my money out the window???
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