2007 ford taurus 3 codes 1 random cylindar misfire 2 # 2cylindar missfire and 3 idle air ckt?

The car has had an exhaust leak and sparatic idle for a couple years just did a tune up a few months ago has 143k on it... I took it to the dealer and asked them to re flash and update pcm they said its already up to date.. now its running like hell today please help what's the deal with it? The dealer also said thry couldn't fig it out....