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I just changed the plugs on my 03 250 5.4 and replace a couple coils. This seemed to smooth out the engine well and turn of the engine light. What I have noticed is that when I speed up everything shifts fine and goes as it should. Then when I go to lightly hold on the gas to maintain speed it seems to stay in to high a gear. If press lightly it doesn't accelerate much until press a little harder then the RPM's jump to a more reasonable level for accelerating. I can also seemingly take my foot off the gas then re-press the gas to get it to accelerate normally again. Whats up?
What it could be is the way the trans decides when to shift. The transmission determines it's shift points from, among other things, the amount of torque being delivered by the engine. With the engine running poorly it may have been down-shifting earlier. Now with the healthy engine it may be staying in the higher gear longer because it detects more torque available. Just put your foot down harder and it will down-shift sooner.
In my opinion the stock coils should be fine on a stock engine. High performance coils may have the ability to go to a higher spark voltage but in reality the spark voltage is determined by the lowest voltage that can energize the plasma arc between the electrodes. If it fires at 10,000 volts with the stock coil it will fire at 10,000 volts with the fancy coil. It's when you make modifications that require a higher voltage that you may need an upgraded coil.
99% of people who swap out their COPs with aftermarket end up going back to OEM. It doesn't matter what the new brand is. OEM COPs are simply better with fewer failures