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Okay, don't take this the wrong way guys. But what in the hell does a transmission have anything to do with a missing/skipping/hesitation symptom? I know that in my twenty and counting years of wrenching, now almost the last thirteen of those years wrenching at a Ford store, I can tell you the number one worst enemy to any automatic transmission is H-E-A-T. And heat is what causes transmissions begin to slip, delay in engagement, delay in upshift, shift harshly, engage harshly etc. etc. etc. THOSE are automatic transmission related issues. And I don't even touch transmissions.
Stupid question. I know that beginning in '05, the Navigators switched from the 32-valve 5.4L to the 3-valve phaser equipped engines that are used on the F-Series trucks as well. HOWEVER, on the Navigators, they still specify 91 octane fuel. Are you using 91 octane fuel?
As far as tuning it up is concerned too. Be prepared to pay a hefty price for your tune up as well. Because if those spark plugs are still original, you can bet that one or few of them are going to snap off into the cylinder head(s) upon initial attempt to remove. The '04 to early '08 model years of the 3-valve engines were the ones prone to spark plugs seizing into the cylinder heads.
m-chan68,
I stopped using 91 octane at least a couple years ago. I never noticed any difference. Ya the tune up is costly $700 +. The tech at Ford explained that they do tend to sieze up. I don't know why they didn't mention that before. With only one exception for converters, my vehicle has only been serviced at Ford.