This is important to understand the likely source of this problem. On the V6, cylinders are paired using the same firing circuit. Therefore, which two cylinders are affected gives some information.
For the V6, the cylinder pair is 5-1, 3-4, 2-6.
SO...if the coil pack for cylinder 5 were bad, then cylinder 1 has to be affected as well.
Since the cylinders affected are not paired, we should look for things that could affect one cylinder or the particular combination.
My vote is to rule out an accidental swap of 2 and 5 at the coil pack.
Next check the routing of the spark plug wires. Did you follow the factory routing including using the stand off's and loams?
Next try this old racer's trick. Run the car in a totally dark location. Look for the blue hue of escaping spark. Inspect the wires for white marks which is evidence of arching.
Don't assume because the wires are new, they are good. If misrouted and arching, it doesn't take very long to ruin a new set of wires.
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.