My Protege 1.6L from 2001 experienced a similar issue. The car's engine has been acting up, particularly in heavy traffic, with poor performance and sudden shutoffs when completely warmed up. The check engine light finally turned on, so I took it to Autozone to get the codes. The codes were P1141 for the back O2 sensor and P0300 for cylinder misfires that seemed to happen at random. After reading this topic, I removed the mass air flow sensor and cleaned it with non-chlorinated brake cleaner as described above. I then cleaned the throttle body with its designated cleaner. The IAT sensor's tiny "bulb" was, in fact, quite grimy.
The check engine light turned off tonight, and the vehicle did feel better, but I won't know for sure that the issue has been solved until I've driven the car for a few weeks, since it only occurs seldom. If I don't provide an update here during the next two months, you may assume that a thorough cleaning of the MAF/IAT resolved the issue.