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Tunes don't change but factory PCM's have more than one - if one of them isn't right for your motor....boom. I don't know much about Ford computers but I would bet there's a normal MAF-based tune which operates in both open and closed loop depending on coolant temp, O2s, etc. and also a speed density tune as a backup in case the MAF fails or some other "limp home" condition occurs. If this is all the same for Ford as it is for GM, the speed density tune probably uses static VE tables to calculate fuel requirements in response to MAP, RPM, TPS, & IAT readings. Most tuners only dink with the MAF tables because it's relatively quick and easy. They rarely adjust for open vs. closed loop operation on a race car - these are two different tunes and will produce different dyno and afr readings, at least on my car. Speed density mode is a completely different tune yet again and is a royal PITA to even get close on a heads/cam motor. Time is money...if you paid your tuner less than $500 he didn't touch the speed density or open loop parameters.
A full-on 350hp race motor running on a stock 220hp VE table due to a sensor failure or burnt wire would probably melt down about like yours did. Something like this should have thrown an OBD code though...you haven't mentioned one so I'm assuming it didn't. Regardless, I would do some research on all the possible reasons a Ford computer could suddenly pick a different fuel map from what it was using on the dyno. Maybe testing your master disconnect threw it into a different base fuel map and it didn't revert back to the "good" map quick enough?
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I'll let Marshall explain, but in short, Ford PCM's work nothing like GM's. And I mean nothing.
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Casey,
I did get a check engine light before the "boom". I'll have to go back and pull codes to see what's up...
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I would suggest looking for a used factory motor and preferably some sort of crate motor-I don't know the power that you need to make or the power that you can get one from the factory. I'm of the opinion that for what we do the failure rate or longevitiy on a new/used motor from the factory is so much better than after they have been rebuilt.
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Maybe it was the steeda ultralight pullies?