If I were you, i'd be looking at the air flow meter. Very common fault on these. And the tricky thing is, it won't always turn the MIL on. Although from what you've described, the auto could be a cause also but not likely as i've never had any problems with them ( I'm a pro-tech at a Toyota dealership by the way ). It would be a good idea to check the auto oil level because as you may know, the oil will expand as it heats up which may be why it seems to be better when its warmer.