What did the old spark plugs in #3 and #4 look like?
Did they show oil or carbon build up?
How many miles on the vehicle/engine?
The coil pack only has 2 coils inside:
Ford uses the "Waste Spark" system
#1 and #4 use the same coil, #2 and #3 use the other coil
So the spark plugs in #1 and #4 both fire on each 1 revolution of the crank, one will be on compression stroke the other on exhaust stroke, so one spark is "wasted"
Same for #2 and #3
I would rent/get a compression gauge and remove all spark plugs then do a compression test.
Write down results
Compression is a fixed result, it can't be intermittent like spark or fuel, so you won't waste your time chasing spark and fuel issues if it is a compression issue.
If you can rent/get a fuel pressure gauge at the same time you can also take off the table, it is another you got it or you don't result.