It sounds like the first step would be a reset of the ECU. The light flywheel and exhaust changes will affect the fuel mixtures at idle or when coming in/out of gear. Disconnect the battery and let it reset completely, then reconnect and drive around some going through the gears.
I agree that it "sounds" like a vac problem, but none of the work you had done should have touched any vac lines. Just sounds like it hasn't learned the changes yet and can't hold the idle when the RPM falls too low.
You should have a CEL by now too for sure... I'd run the codes on 'em all...
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