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the wiring diagram im looking at does not show a relay for the maf, when your trying this maf it is hooked to the intake with no air leaks isnt it? any air leaks sends these things crazy also cooling fans have a real bad effect on them while testing, Pink wire is your power feed and the black wire is ground, ground should have less than .2 ohms resistance and the power wire looks like it should be battery voltage on this model, usually they are only 5v. The power wire feeds several other solenoids, a.i.r. etc. so if you dont have battery voltage at the pink wire check your eng 1 fuse, if one of the other solenoids is shorted it could pull the voltage low to the maf and cause a bad reading, hope this helps...
Sounds like you might be affecting the fuel/air ratio mix. Just on a long shot, check the CHT sensor and the connections on the front of the water pump. This will affect the running of the engine and make it very rough due to a over rich condition.
This is a speculative guess but if this condition existed, I believe it would throw a code 14 or 15. I hope you checked for codes for it might point you in a direction.
And last thoughts, I would also check the action of the TPS for smooth operation as the throttle is opened. And any poor connections at the PCM connectors.
Thanks guys, i found out that the rough idle was due to a leak in the intake air couplers between the MAF and the Throttle Body. I must have torn it while changing the MAF. crap.
However now i'm back to the original problem of her having a prolonged stumble, pops and backfiring if i dont warm her up for a minute or so.