Low RPM misfire from 1k-2k RPM's PLEEASE HELP!!! Frustrated

Here is the entire story from when I got the car and what it is doing now. I bought this clean 99 GT and there was a minor low rpm misfire but that was the only thing wrong. Well it has just got a little worse I think. It is sputtering and hesitating in low rpm's from 1k to 2k rpm's and is more evident under heavier acceleration. Then above 2k rpm's the car seems to run fine and I cannot notice the miss.

So the other day I took my Predator tuner and removed the diablo tune and set it to factory backup.. I then tried adding some seafoam to the vacumm hose on the rubber intake that connects to the upper metal intake and realized it did not have enough vacumm. I filled the car up with premium gas also and it seems to be doing worse. I then re-installed the diablo tune and removed the EGR valve in custom tuning. I then cleaned the MAF with electrical cleaner.

The car is still sputtering and there are no CEL on. The only code it reads is p1000, not sure what it is. The car has 100k on it and has the following mods in the signature. Has anyone else encountered this low rpm miss and how can I fix it. i am really frustrated with it. Thanks in advance!
 
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Have you pulled your Coil-over-plugs out and checked for signs of water /rust in the plug wells??? This is common on these engines. You may have a bad COP. Try pulling the electrical connector off each COP one at a time until you don't here a change ie the misfire doesn't get worse. Thats one way to find out which one is bad. Have you changed your fuel filter.
 
The problem seems to geta little worse when the car is warmed up. Does that mean o2 sensors? If it was a fuel pump wouldn't it be starving for fuel at higher rpms? I am not throwing any codes for 02 sensors. I have checked for vacumm leaks and could not find any. Help!! I am annoyed by this situation.
 
if you floor it from 1000rpms and it still sputters then it isnt the 02s. the car is in open loop under WOT so it ignore the o2s. a p1000 code just mean that it hasnt completed a drive cycle for the emissions stuff. it doesnt have anything to do with your hesistation. i think spark would be the next thing to check out. could be timing or it could be a weak coil. change plugs and when you pull the COP test the resistance of each one and they should be all around the same resistance.
 
Alright well the car is now missing a little up high past 2k. It is also idling slightly rougher than before. All of this really started when I reset the ecu with the tuner and added seafoam. Even before this I noticed a slight low rpm miss but now it is much worse. I will change the fuel filter tomorrow and report back. Where is this located and do i need any special tools to change it out?
 
from my experience, ignition related misfires a more prominet at low rpms and high load. how many miles are on your plugs? a good (and cheap) replacement are autolite 764. if new pugs don't help, it may be one or more COP's gone bad
 
Update: I changed the fuel filter and no change, the problem is still there.

I took the predator diablo tune off and set it to factory backup original just to be sure it was not skipping any codes.

How do I check to see which cylinder is misfiring? Should I unplug each cop connector while the car is running and note which one has no change?
 
Update: I changed the fuel filter and no change, the problem is still there.

I took the predator diablo tune off and set it to factory backup original just to be sure it was not skipping any codes.

How do I check to see which cylinder is misfiring? Should I unplug each cop connector while the car is running and note which one has no change?
You are better off pulling the injector plug for each cylinder. Pulling the cop will cause the cylinder to load up and could foul the oil if it leaks down.
 
UPDATE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

I restored the factory backup with the diablo tuner and drove the car around and finally got a check engine light. It is 308 which says cylinder 8 misfire. Does this mean coil or plugs? I bought 8 new Motorcraft SP-493 plugs and got some antiseize and the silicon grease for the boots. I have an extra FMS coil pack as well. I am going to go ahead and change allt he plugs due to the mileage on them. My question is, which cylinder is #8? Also do I need anything else for the plug change? Should I use the antiseize and silicon grease? Thanks for the help guys.
 
it could be either. a code doesnt tell you directly but a good start would be changing the coil and plug. and idk about the plugs. i always got NGK's. im sure you can find out on the net if theyre the right plugs