2001 LS- Bad Misfire/Flashing Engine Light/Long Crank

2001 3.9 LS Misfire/Flashing Engine Light- This issue has gone back quite a ways but it had been misfiring before and the check engine light would come on solid (ths misfire was slight) and so I took it in to have it read and was told I needed new valve cover gaskets and coil #3. There was a lot of oil down there and so I replaced it all myself along with the spark plugs and one extra coil that looked like there was a lot of oil on the boot. It didn't solve the problem as there was still a slight stutter. Had it read again and now #2 was showing up. Replaced just the coil this time (and looked at the others to see if there was oil down there and there was very little anywhere). Still didn't solve the problem. I let it go for a little while because I couldn't afford to keep guessing and being wrong (or make that the dealer). Now it's gotten to the point where it's running really rough both on idle and accelerating (it's especially choppy between 2000 and 3000 RPM). It seems like multiple cylinders. The check engine light now flashes, goes solid, flashes and so we ran the scan tool on it again and this time it was showing an N/A and #6. I had 3 new coils ordered and decided to change #6. Once again it didn't solve it (still running as choppy as ever) and now it's saying #4 but it still seems like multiple. On top of that, I should add the car has had a long crank on and off for quite some time that the dealer couldn't figure out and has a gas smell afterwards sometimes when it starts. The dealer checked the fuel pump before and said it was fine and I have replaced the fuel filter.
I have run 87 in it from the past couple years and am wondering if it could maybe be the injectors or if I shouldn't be doing that? Most I've talked to felt it didn't matter. If it is the injectors, how could I tell? I have run fuel system cleaner before but didn't seem to make a difference. Any thoughts would be extremely helpful.
Thanks!

It is, unfortunately, very common for coils to fail on the V8 LS, with and without oil on them. Your first troubleshooting step should be to replace all of the coils. You should also clean or replace all of the plugs again, because of the misfiring coils allowing them to foul.
It seems that once the LS gets to a certain age (mostly the number of start/stop cycles), that all the coils will start to fail, one after the other.
I think there is a TSB on the long crank that recommends that new code be flashed into the PCM.

I agree that you probably need to replace all 8 coils. If you did the valve cover gaskets, you certainly have the skills to replace the coils yourself rather than going through the dealership. Heck, even if you didn't do the valve cover gaskets yourself, the coils are pretty easy on the V8. You probably just need an 8mm socket and wrench. If you have an O'Reilly Auto Parts nearby you'll likely find coils for your car are about as inexpensive there as anywhere (including online). They can also read the diagnostic codes for you.

If the Check Engine Light (CEL) is flashing you NEED to address the issue before it also destroys the catalytic converters. If you think the required 91+ octane fuel and coils are expensive, you'll be shocked with the price of converters.

You could also clean the Mass Air Flow (MAF) sensor with the appropriate cleaner and verify that you don't have any vacuum leaks. Either of these could cause the sensation of misfires. I'd also suggest you use a can of SeaFoam in the "Cylinder decarb" process. If you've been running with misfires and low octane fuel there could be a fair amount of carbon in the cylinders.

And finally, spend the few extra pennies per gallon and run the premium fuel, not only will the car run better, it will lower the likelihood of damage to the engine caused by pre-detonation. The engineers didn't just specify "Premium Only" to get the power numbers up....

-Rod

Not everyone can afford throwing parts + service at a Lincoln.
$3.5K for Auto service practice, the root cause was a bad fuel filter for random misfires. See http://www.Lincolnforums.com/forums/index.php?showtopic=5675

Not everyone can afford throwing parts + service at a Lincoln.

Agreed, but if the valve cover gaskets were leaking as bad as it sounds like they were, replacing all the coils now may reduce a lot of headaches in the future. O'Reilly has them in stock for $50 each. Yeah, $400 is a lot of money, it comes down a bit to how much the owner's time is worth.

-Rod

Ok, thanks for the info. We pulled the plugs for #1 and #5 (was reading P0305 and P0301) and put a new coil in #5 and one we thought was still good on #1. Both plugs looked fouled out and since it was late, we just cleaned them up and put them back in. After getting it going, (still missing) and running the scan again, it came back with #5 again (and an NA on the first code- probably still #1). I guess my next step will be to replace those two plugs and go from there.

Any evidence of oil on your COP boots could cause a misfire, how many Sparkplug boss seals leaking? (1 & 5)
The contaminated COP's canbe cleaned with CRC electronic cleaner.
If only two boss seals are leaking, one on each bank, you can make a condom to help protect the Spark plug terminal from shorting to ground.
If theres two blown boss seals on the same bank, replace the valve cover gasket + Sparkplug Boss seals on that bank.

All 8 coils should be the same, you might try switching coils and plugs between various cylinders on the same bank. See if the misfire codes follow the coils, plugs, or stay with the same cylinder. Mix them up and track which of each went where. You could have two bad spark plugs giving the misfire codes as well, so don't move the coils and plugs to the same cylinders.

-Rod

ever figure out what was causing the misfire in your ls?

I've had all the common misfires with my LS. I've had my car for 5 years now and I've replaced 6 coil packs...grrr cuz it's only a V6. But this last one kinda confused me due to the fact it was not allowing me to get my RPMs over 2500 so had to go check the codes that came when fail safe happened. P2107. It ended up being the throttle actuator control module. So I went to a recycle yard and got one for around $60 and replaced it...very easy! The car would then have proper RPMs but still misfire under a load so check codes again...P0305 which I've replace in 2008 so super easy and thanks to Rod, O'Reilly's had it on hand for $54 which saved me some money. This one was on the driver side, thank GOD, so no taking off the intake. To sum this up, my LS is running great...finally!