07 Yaris Sedan rough idle after sitting

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So what I have here is a 2007 Yaris Sedan, the unit has roughly 198K miles on it and generally runs like new. But over the last year I have started to notice that after the car sits unused for a couple of days (think parked on Friday after work and not started until Monday morning) the unit wants to run rough. The problem is compounded if I have to start the unit for a very short period of time (think moving it a couple of feet to access a work bench in a garage) and shut it down in under a minute. The issue on Monday morning is 10x worse and possibly takes 3x as long to get started. This morning was one of those bad ones and started but ran rough, I then noticed for the first time with this issues the CEL was illuminated. Anyone have a suggestion on where to start or what might be the problem.