Ok, I have a 2001 ford ranger 4x4 with a V6 4.0L Engine. I am getting a cylinder #3 misfire, I have a new fuel pump, new fuel filter, new plugs and wires and coil pack as of 1 month ago. Heres how it happened in order.. I started it in the morning and it wouldnt even get out of the driveway I had 3 total misfires.. Then I went back to look at it 4 hours later and let it run. It started running much better and seemed to clear itself out. I found this very odd. I got the code checked again and now I only have one misfire on cylinder #3.. It comes and goes, and it mostly happens during idle rpm or below 1,000rpm's.. Its very bad sometimes, and very slight sometimes, and sometimes its never there at all.. I ran lucas fuel injection cleaner through it with no luck.. Any suggestions?

 

I'm thinking it's electrical. Are you confident in the plug wires you used and that the installation was correct? You may want to swap the #3 plug wire and see if you get any improvement. (see the solution on "Cam sensor help" on this forum)
When you say it misfired three times when you tried to drive out of your driveway, what did you mean by misfired. Was it like a backfire? Did the engine just quit for enough time that you realized a drastic hesitation? I am asking this because I wouldn't think you would notice one cylinder out of six misfiring when slightly above idle. I don't think I would notice it then.
Did any of this happen immediately after the work you did? Do you see any correlation between what you did and the work that was done?
Do you hear any sticking valves (noisy) when the engine is cold? Can you isolate that noise (if any) to the #3?
How many miles are on the engine?
You can guess what I am thinking from the questions I asked. These are areas I think should be investigated. I'll give details when I have answers to the questions I've asked. Thanks and good luck.

 

Had the same problem on a 2001 sport trac. replaced everything having to do with ignition and mapping.

finally went to replace the fuel injector. the "seat" or "nozzle holder" was cracked in half. causing a vacuum leak. same issue you had problem would come and go, sometimes bad sometimes not bad at all. its around $6 at a dealer.