I've owned bunches of the 4.6 Ford V8's in Lincoln form and Crown Vic, and I'd bet money its a coil issue. Often, the coil itself is OK but the rubber boot has a weak spot that allows the spark to jump to ground and cause a misfire.
The simple $20 code readers on Amazon or the ones AutoZone or O'Reilleys uses will read the codes those types of misfires set. I paid $20 for mine on Amazon, and it connects to my I-phone via Wi-Fi and reads the codes. The last time I had a bad coil, it told me which cylinder the misfire was happening on.
Like any mechanical item, those cars won't last forever but the Crown Vic / Marquis / Town Car vehicles are far and away some of the most dependable, economical cars on the road today. I drive an '09 Lincoln MKS now with a V6, and even though it's been a great car, there's still something I miss about a good old-fashioned rear wheel drive V8.
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