Just a thought; you should Mercon LV. Ford automatic transmissions have been known to fail because the wrong fluid was used. Not to say that you have to use Ford Motorcraft brand. You could use other brands which meet specifications, or are Mercon vLV licensed. But you do not want to use just any type of ATF sold over the counter.
When Ford began using Mercon V, a lot of people were buying Dex/Merc ATF and/or multi-vehicle ATF. Those ATF do not meet Mercon V spec. Those transmissions failed.
The 6F35 uses a low viscosity fluid. Be sure that your choice of ATF is labeled for Mercon LV. Most of the over-the-counter ATF are not Mercon LV spec. It's not too late to correct this. And be sure that you perform a triple drain & fill, or a transmission return line exchange. I cannot stress how important it is to have the correct ATF.
Glad that you got some new spark plugs and coil over plug ignitions, and that it worked out.
On that note, what brands did you use? Did you stick with Motorcraft, since it's what most people recommend? The common theory is that Ford engines operate best with Motorcraft plugs and ignitions. I don't buy it. I think that there are brands which may not work well, and then there are people who buy less expensive spark plugs. To save money, some people will install the least expensive spark plugs. Commonly, that would be a copper spark plug. Not a great idea when your car came with finewire platinum, double platinum, or iridium spark plugs. The other common mistake is to use spark plugs right out of the box, without checking the gap. Some plugs say that the recommended part number for your application is correct, and that you are not suppose to change the gap. Then there is the controversy that today's modern engines and modern spark plugs do not require anti-seize. Then when you're looking at coil over plug ignition, Motorcraft can cost up to 3X as much as a product which you've never seen or heard of.