Hi, ive no idea why the engine stalls, hopefully compatible lambdas are fitted and the electrical connections are okay ? Replacing the exhaust won't stall your engine. As u say u had it fitted the question is what else has been touched ?
But with the high idle speed that is possibly due the engine is breathing better after fitting the Y pipe etc, and so the EFI ECU recognised this, as it does.
Its something that I had on initial start after I fitted a Janspeed CAT back system, the revs went up to 2500-3000 for two minutes, then dropped back down to 1000 and then onto its usual 650-700 rpm as it normally does on a cold start, so the ECU readjusted and sorted itself out, that was 12 years ago and never missed a beat since.
So if you can get your engine to run longer, at least a couple of minutes the high idle speed will drop.