That is how a car runs with a missfire.  Most likely one of the COPs,
even though you say they were all replaced, they can still fail
prematurely.  What is the engine code that is given for the missfire?
If is just one PO30x (x = 1 through 6 corresponding to cylinder) swap
that cylinder's COP with another cylinder and clear the code.  Start it
up again and see if the code changes to another cylinder.  If so you
have a bad COP or plug boot, but they usually come together I think.

Don't drive the car until this is resolved.

Have you had the "reputable guy" check his work to make sure he has
not damaged a wire somewhere? Or have him uninstall it to see if that
is the problem?

Integrated EFI systems are the sh.ts, aren't they?  Who decided on black
boxes running fuel injection, ignition, and charging systems with wires and
sensors running all over under the hood and dash?  That's stupid.  In the
old days, cars were easy to fix.  Just ask your grandpa.  His cars didn't
have a single CPU in them and they still got him from point A to point B
just as good as your late model heap, when it runs.

So here's how to get your late model F-O-R-D fixed without having to keep
paying over and over again while the incompetents replace parts ad lib
until they accidently strike upon the problem, if ever.

When you take your monstrosity to the Ford Dealer, have the work order
written:  "To replace  part(s) x and y to fix problem of cylinder
misfiring, for $$."  If he's not so cock sure what your problem is and
wants to make a preliminary diagnosis for a fee, that's okay.  "To
diagnosis the problem of cylinder misfiring, for $$"  That way, when they
replace x and y to "fix your problem" and you still have the misfire when
they're done, they have to fix it again for FREE, taking out x and y and
putting back in your old parts if possible.  And if its not, the parts are
free and they keep having to fix it until its fixed or your money totally
refunded.  Don't feel sorry for the dealer.  He's not sorry you paid six
times and its not fixed yet.  If he cries on your shoulder, tell him its
Ford's fault for making their cars non-fixable therefore he should vent his
complaints to the Corporation, not to you the poor sucker who bought this
junker.

Birkshire Bill wrote:

This isn't what I meant.  The owner is not telling the service manager
anything other than the complaint; ie, misfiring.  What is happening is the
service writer takes a stab at the diagnosis, either with or without his
mechanic's evaluation, and writes up a work order, listing parts to R & R
or adjustments to make or whatever.  Then he has the owner sign the work
order.  The work is performed as written and the owner pays.  Even if the
problem persists, the owner has little or no comeback to the dealer because
the dealer did do the work.  What I suggest is after the service manager
writes up his work order, the owner has him add the phrase "TO FIX THE
PROBLEM OF MISSFIRING (OR WHATEVER).  Then, if it turns out to be a
misdiagnosis on the part of the all-knowing service writer, its his
problem, not the owner's to pay again and again until the problem is fixed
or the owner gives up and trades in his car.  

The idea is to pay for fixing the problem; not to pay for a laundry list of
procedures that don't fix the problem.  If your shop uses an amateurish
shotgun approach of wholesale parts replacement and refuses to commit
itself to a solution on a given work order, then find another shop.  If its
a dealership, complain to Ford.