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2002 Sequoia here; I had this problem with a battery disconnect a couple years ago, and limped to the repair shop. They cleaned the MAF sensor and throttle body which seemed to resolve the problem. I had the problem again just this month (another battery change), replaced the MAF (I did have an oily K&N filter for a long time) and cleaned the TB myself - no improvement. Computer was throwing codes this time; checked codes: ECU general whining, random misfire, cyl 1 misfire, cyl 3 misfire (once). Moved coilpack from Cyl 1 to Cyl 2, checked codes again and cyl 2 was misfiring now. Replaced coilpacks 1 and 3; problem solved.

I'm sure there are other things that can cause similar symptoms, and this is not proposed as a complete solution for everyone, just my experience. OBD Fusion on the iPhone plus a VeePeak OBD scanner were very helpful. I suspect this was the problem a couple years ago too, but just got lucky. If I weren't so cheap, I'd replace all the coilpacks, but at $55 each for Denso, it adds up. I have a spare at least now.

Why disconnecting the battery would stir this up, I don't know. Possibly the ECU trims had gradually compensated for marginal coil packs, and couldn't get back after losing the settings suddenly.
 
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