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I just swapped a 2002 4.6l 2v sohc into my 98 gt. For the most part everything went pretty smooth except it didn't pass emissions. The test showed that cylinders 1 and 5 were miss firing and that the motor is running lean. I figure the old 98 ecu is reading the new motor wrong so i'm thinking about ordering a diablo sport tuner the fix the air to fuel ratio. The motor hesitates throughout all rpms. I'm assuming it's because of the missfire..? Any help on where to start with fixing the missfire and whether the tuner is a good buy would be appreciated thanks!
 

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I think you would have to swap the 02 computer over to the 98 too, wouldn't you??
 

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Don't try to swap in a 02 PCM into a 98. It won't work. Keep the electrical from the 98.

IMO, you are not passing because of the misfire. Fix the misfire, and things will be different.

Double check the routing of the spark plug wires. Cylinder #1/#5 share a coil pack secondary circuit. Start first by confirming spark in 1/5.

Next check the low voltage primary side of the coil pack. Check the connector to be sure there aren't any bent/pushed pins.

A noid style test light can be used to confirm there is a firing pulse from the PCM.

The turner would provide very helpful diagnostic information. Having access to ODB2 operational data will make this much easier.

IMO, the usual cause for lean is a vacuum leak, exhaust leak, or dirty MAF. Start with the simply things first before flying off the handle.
 

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There's an error in the reply above. Sure wish we could edit our posts.

The 96-98 V8 coil pack cylinder pairing is:

1/6, 3/5, 7/4, 2/8.

So cylinder 1 and 5 do not share a coil pack. However, they are next to each other.

As mentioned previously, check the spark plug routing. IMO, it is likely that #5 and #1 spark plug wires have been installed reversed at the coil pack. That would cause a misfire in both cylinders.
 
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