Replaced all plugs &coils still missing bad - 2001 Lincoln Town Car

Changed the coils on 5 & 6 ?

They may not have been the failed ones at all

You may have all 8 bad, after they been in the
motor for 6 years or more

You can not go by obd codes for a cylinder misfires
on a Lincoln L/S

I have a 2004 L/S V8

I do not have the time to type all night & teach a class,
on how to solve that issue

All you can do is walk one new coil until you find the bad one
or several

If you ever go into ETC Fail safe-- do not replace the throttle
body-- it will be a bad coil

As you have tried to do--I have seen a PO300 codes indicate a failed coil

I have used Mode $06 on professional scan tool to find failed coils

I have had to walk a new coil & replace the old one & move to the next cylinder, until all issues were resolved

That car is unique to anything you will have to work on

A quick way to check the single coil pack if you know for sure which cylinder is miss firing and its setting a code you can swap the coil pack to another cylinder and see if the miss changes from one cylinder to another. If it travels to where you moved the coil then the coil is bad,if not you have other problems.

If you changed an individual ignition coil based on
a PO305 & that didn't resolve the issue, then either
the code didn't help & you have a different coil bad or
several

Put back the old coil on #5 & check codes again & walk
a new coil until you get the bad one or more

If you have a shop put a scan tool on it-- use Mode #06
to check misfire counts

Sometimes that doesn't get a really hit & miss coil & your
back to walking all those coils not replaced in the last couple
years

What codes do you have?

You use the codes & diagnostic manuals,
to decide what testing to do,not replace anything at all

Spark plugs seldom go bad or fail to fire,maybe never in
your lifetime

I may be the exception, but never replace plug wires.
If you have a used vehicle & depend on a repair shop
that too many hands abused them, then change them

The idea is to use professional tools such as reference
material & an oscilloscope to look into things & spot a problem
part,then change it

Now your coil for #4 may have not been the problem
A code for a misfire such as a PO304 but not the coil causing
it or a different coil spiking the pcm/ecm & giving you all sorts of
misleading codes

You could have a bad injector on#4 or a vacuum leak on injector
& you go down the trouble chart or tree on your reference material
& continue testing

I can write a book but can't diagnose without the vehicle

You either go to Helm.Com and buy the necessary manuals
or go to a repair shop to have them do other testing, keep in
mind they know not to do the plugs,wires etc you did

There are shops that will throw parts at it, then ask for you
authorization to continue, they should be working only on the
main problem you go there for,then you build the relationship,
if they prove they can solve your complaint

Causes for a cylinder misfire include. Bad spark plug, bad spark plug wire, bad coil ( or coil pack) if no wires, Bad fuel injector..I would start in the order I listed.

Do you mean P0301, P0302, etc? Misfire codes? You have 6 plugs, 3 coil packs, and 3 wires. cyl 2,4,6 are the ones in front, with the coil packs. It's possible they're bad.

You still have random misfires (PO300)
You most likely replaced those coils that set a code, and those were not the one bad offender,spiking the computer module.
Take a new coil and put in a cylinder,no change, replace old coil and move new one to next cylinder. You can do that once or twice a day, if you have nothing else to do. You need a 90 degree day, to really get that solved,unless you have an ignition oscilloscope.
Never had a bad spark plug in 45 years.

is the car missing when driving? 2000 and on has coil over plug's there are no wires. Is the check engine light on? if so go to an Auto Zone parts store or one that will scan the car computer for free and get the codes out to pin point the problem. Sounds like the cars miss firing. it could be more than one coil and or plug going bad. Did you replace any coil packs? Bad coil packs are 90% of all miss fires on todays cars and trucks.

The coil itself could be bad.
Try determining if there is a miss on a cylinder or cylinders.

I would remove one plug at a time, plug it back in wire and lay on top of engine block. Have some one crank and look for spark. Do this for each plug. If 1 is missing. You have bad wire. If two sparks are missing, then you have bad coil pack, if 3 is missing, you have two bad packs or bad module, if all cylinders are missing, then module or cranks sensor is faulty. Dont forge to change those plug wires just as often as plugs. They may look good still, but they get weak