kevinclee, regarding the clicking noise from the engine. From inside the car, the noise reminds me of the clicking sound a diesel engine makes at idle. Sort of a rapid tick, tick, tick. When I mentioned it to the shop foreman at the dealership, he said the sound was coming from the fuel injectors because the engine was set back on the chassis close enough to the firewall for the sound to come through.
Regarding the engine management programming. The problem with the original programming was a sporadic tendency for the transmission to "hang"; to start to shift, to hesitate, then sharply engage the gear on the 2-3 upshift. The dealer checked and said my car didn't have the latest update and that they would re-program the engine management system, which essentially raises the rpm at which the transmission shifts into the next gear. To my mind, it hasn't made the transmission shift any smoother, although the "hanging" problem is less frequent, but still there.
I was merging onto the interstate yesterday, floored the gas to get up to speed to blend into traffic and nothing happened! I released the gas pedal and floored it again and it finally kicked down to a lower gear. Unreal.