The random misfires problem occurred on my '01 4.0L for quite some time and no matter what I did; the problem persisted....
Several months ago I needed to replace a badly worn clutch throw out bearing.
At the same time I replaced the clutch, pressure plate, flywheel and cleaned the transmission shaft.
While replacing the flywheel I noticed the CPS triggering blocks had a lot of surface rust and the CPS had rusty dust on the pickup surface.
I wiped off the rusty dust from the CPS and the new flywheel CPS triggering blocks were rust free.
Since that time the random misfires have disappeared other than a brief period when I found the #1 spark plug misfiring which I cured by replacing the spark plug.
Remove the CPS and inspect the CPS pick up surface for rusty dust or metallic dust and try to inspect the flywheel triggering blocks for rust thru the CPS mounting hole (difficult to see, but it can be done).