A cylinder needs 3 things to fire... Fuel, Spark and Compression... sounds like you've got 2 of the 3 (mostly)...

Had a very similar situation w/my 4runner... turned out to be injectors were clogged due to PO neglect... sent them out to Cruzin Performance and bada bing, no more running on 2 cylinders... you didn't say if this vehicle was a new acquisition or one that you've had for a while... its also a great opportunity to change out the fuel filter too...

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Dave
86 4Runner, 22R-EB