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.

Let me say hi and also thank everyone in advance for any help given.
Here is the problem.

My father has a 2000 ford taurus.  Car never gave him any problems.
Out of nowhere he now gets a cylinder missfire in cylinger six.  That
is the error given by the computer.  Not that simple though, there is
more.  The car runs fine until it warms up.  When the car is idle, in
either park, neutral, or drive, it starts to chug.  The check engine
light flashes.  As soon as start to move again, the car struggles to
accelerate, but once your moving, all is well again, the car runs
perfectly fine.  Check engine light stays on steady now, until you
stop again, and the cycle repeats.  Just a little helpful information.
The car has been to three different shops, including ford themselves.
The plugs, wires, coils, fuel rail, fuel injector computer and so on
have all been replaced.  The engine was opened up, and the cylinder is
fine, nothing wrong mechanically.  This is absolutely 100 percent an
electrical problem.  So with this said, does anybody know what the
heck this could be?....Ask me questions if you want any more
information.  

With all that information, I will now tell you the the car had an
aftermarket remote car starter installed by a reputable guy that has
installed stuff for a dozen people i know.  The problem started about
one to two months after that.

thanks again
Eric