We put in Motorcraft plugs 2000 miles or so ago. It stopped all the jerking and the Service Engine Light went out and ran great but a little miss.
I don't know if that little miss is gone for sure it has done this before ran good a day or two then started back up.
Using a code reader, clear all old codes. This will reset the PCM and it often makes a big difference. This may help eliminate any remaining miss.
With regards to the EGR, soft hoses should definitely be replaced. EGRs are notorious for causing poor performance. Also, be sure you replaced the PCV Valve at 100,000 miles, along with the Emission Separator. The setup should be similar to what's described in the link below:
https://www.askmehelpdesk.com/cars-t...ml#post1375837
When you apply dielectric grease, apply a light coating to just the terminal nut and porcelain insulator/corrugations, not to the ground electrode or center electrode.
I recommend you only use full-synthetic engine oil in your Mustang. Change it, along with a premium oil filter (e.g. Mobil 1 or Purolator Pure One), every 6,000 miles or 6 months, whichever comes first. If you have an automatic transmission, be sure to drop and clean the pan, change the filter, and refill with Mobil 1 Multi-Vehicle Synthetic ATF every 30,000 miles. Here's how to easily do a superb job:
https://www.askmehelpdesk.com/cars-t...ml#post1873132
Starting Tip: Turn the ignition switch to ON--this allows the fuel pump to fully pressurize the fuel rail. Wait until you can hear the fuel pump, located in the gas tank, stop running. Then, turn the ignition switch the rest of the way to START--the engine should fire right up.