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You are the correct, the programmed CID will be wrong but the MAF-based PCM will adapt to the larger engine. That is why I was very specific with my statement "As long as the 5.8L engine is stock or very close to it there is no need to source a computer (PCM) for a 5.8L engine or worry about "tuning"
Once you start adding non-stock equipment then you will be on the edge or beyond of what the PCM can compensate for.
Would there be an issue with me opening up the exhaust from the heads back? If that's enough to put me over the edge I'm going to go ahead and source the PCM.
5.8 + AOD ask for a flex plate for an 89 crown vic with the 5.8 and AOD. There's a flywheel thread in the 80-86 section, FAQ I think or the how to with part numbers.
Would there be an issue with me opening up the exhaust from the heads back? If that's enough to put me over the edge I'm going to go ahead and source the PCM.
I am fairly confident the 5.0L accessories and brackets will work with your 5.8L engine. IIRC Conanski stated the brackets have holes already drilled for each engine.