Glad you got this sorted...
I recently replaced the timing belt, water pump and accessory belts on my 2002 4Runner. During the work, I had disconnected the battery. The battery was disconnected for about 10 days while I performed the job (amongst many unrelated chores). Upon getting everything done, I started the car and it barely ran for a bit and then died. I tried to start it again but it wouldn't start. My first thought is I must have screwed up the timing during the new belt installation. I tore stuff back apart and found my timing to be spot on. I reached in and tried to start the car and it started easily and idled smoothly! Given I didn't have the radiator connected yet, I turned the car off and buttoned everything back up.
I did a web search and low and behold, like the Boxster, the 4Runner looses its smarts when battery is disconnected for extended periods. I did not have an adaptation routine like the Boxster but if I would have just fought it and kept it running when I initially started it, it would have smoothed out within a minute or two. So now I know....
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