Bad exhaust donuts can cause overall poor performance and rough idling. They will go bad, it's a matter of time. I have just shy of 4000 miles on my RX and they're starting to go.
Carbs ever been cleaned? That could very well be part of it also.
If it hasn't been run in a while there could just be some moisture built up(particularly this time of year with cool nights/warm days), and letting it run and heat up for a while can burn it off.