I need your help! 4.0 Misfiring!!

Hello everyone. I have a 2002 Ford Ranger, 4.0 V6, 162,000 miles, automatic, 4x4, xlt.
I got in my truck to drive home from work day before yesterday (25 miles) and I when I started it I instantly could feel the bucking and jerking of the engine. I got out and looked everything over and could not find anything wrong and there where no engine codes thrown. About half way home the CEL light finally came on and threw codes p0135 and p1132, both of them are o2 sensor codes. Well I got home and again looked everything over very closely looking for any bad wires or vacuum leaks and found nothing but I was busy so I had to wait to work on it.
Then my drive to work yesterday gave me some better data. I got p0135, p1132, p0300, p0303. The 300 is random multiple cylinder misfire and the 303 is cylinder 3 misfire. and it was the same on my way home so I stopped and bought a new air filter (just because it needed it anyway) maf cleaner, sparkplugs and wires, and marvel mystery oil for the gas tank.
I cleaned the MAF out really well with the MAF cleaner, replaced the Motorcraft plugs and wires with duralast gold wires and bosh double platinum plugs. The plugs defiantly needed changed, they where rusted, had a lot of carbon buildup over the years and where gapped in excess of .95 !! Well I get her all back together with new shinny plugs and wires and new air filter and cleaned off maf and I thought I would be good to go.
On my drive to work again I get the same bucking and jerking common of misfiring and the CEL is flashing on and off with no codes stored. Well once the engine warms up the light goes off and the engine smooths out, mostly. I can still feel it running a little rough but it isn't that bad. Idle when it is cold bucking and jerking ranges from 850 to 930. I am getting 6 pending codes but none are thrown just yet. I get p0135, p01132, p0300, p0301, p0302, p0303, all pending. So it seems like all of my passenger side bank is missing badly when cold, and moderately when warm.
I am completely out of ideas of where to go from here!!
I am going to swing by and pick up a new fuel filter after work and throw it on there just because I don't know when it was done last.
Could this be a symptom of the coil/ignition pack going bad? Please help me in the right direction! I will post updates as I get new codes or hopefully when I get this thing figured out, thanks in advance for any help or suggestions!

Coil pack?

I was wondering about the coil pack myself but it looks fairly new like it was replaced at one point in time (the truck is new to me so I have no idea) and they run $80 bucks. Also if I "romp" on it the truck as plenty of power and has no problem getting up to speed. Drivability is almost unaffected, besides when its cold and when Im sitting at a stop light and the truck lightly shaking at idle. What are you thinking?

http://troubleshootmyvehicle.com/ford/4.0L/how-to-test-a-misfire-1 http://easyautodiagnostics.com/ford/4.0L/index-of-articles-1

I think that might be exactly what I need. I ll go through some of those tests tonight when I get home and let you know.

On my way home yesterday I get p0135. p01132, p0300 codes and p0301, p0302, p0303 as pending codes. I used my timing light on all of the wires with the truck running and there is definatly a lot of missing going on by watching the flash of light, or it could be that my 25 year old timing light could be missing a few beats. So I went out and bought a spark tester and by the time I got back it was raining so Ill have to do my testing tonight. Ill post later.

Alright, through all the rain and getting a new puppy (chocolate lab) and visiting family I found a little time to diagnose on my truck. Using a spark tester and running the engine while cold I found that the coil was missing every once in a while so I bought a new coil and put it on and also put on a new fuel filter. Then I let the truck idle for a couple hours and it was idling fairly smooth and there was no check engine light.
Well I get in to come to work today and its missing very badly, bucking and jerking and almost dying with the check engine light flashing on and off. Then I get about a block away from my house and the light goes off and the engine smooth's out and I get power back again all the way to work. Then pulling in my parking spot the idle drops to 600 rpm and idles very roughly.
I pulled the codes and I get 10 pending fault codes! p0135, p0300, p0301, p0302, p0303, p3503, p0003, p01<D, B2TAE, ROR. I have never even heard of those last three codes and I have been a mechanic for several years!

I believe p0003 is something to do with the fuel pressure regulator. Could that be the root of my problem, or is it just because I changes the fuel filter and I need to clear the code.
No idea either what p3503 is.
Anyway I also sprayed the engine down with ether looking for a vacuum leak and found nothing. I looked at every vacuum line and every electrical wire and I'm at my wits end here.
So in all Ive changed the oil, new plugs gapped to .50, new wires Duralast Gold, new coil BWD, new air filter, new fuel filter, cleaned the MAF, checked for vacuum leaks, oil pressure is good, TPS is good, Temp gauge is good, voltage and charging is good, grounds are good, MAF is good, rpm's read correctly, its timing seems correct, compression is most likely great because it has loads of power when its the right temperature.
So it appears to me that either all of my passenger side sparks plugs aren't working or all of my passenger side fuel injectors aren't working.
If anyone has any advice here it would be very greatly appreciated!!!

I am not very familiar with the SOHC engines, so I must ask this question. Do you have a catalytic converter on either bank, or are there 2 cats in line with each other like the OHV engine? If you've got one on each bank (before the y-pipe comes together), you may very well have a plugged cat.

It's got one on each side. I would suspect a plugged cat also but when the truck is warm it runs eccelent. Also a plugged cat would only be a symptom of running rich from the engine misfiring most likely. I am going to spend the evening cleaning all of the electrical connections and applying dielectric grease and I'll see if that fixes it.

Well hopefully its something simple like that. If not, I have seen a few engines that popped the head gasket directly between the cylinders, causing pre-detonation(however most were GM engines, go figure). Does it ever spark knock?

I am fairly confident that the head gaskets are good, however there may be another issue causing per-detination. I already made sure that the plugwires arent touching ect. I'm not 100% sure I even know what "spark knock" is but there are no funny noises or pinging at any rpm.

Well today same thing. I filled up with 91 premium chevron and added double the recommended dosage of marvel mystery oil. Then I came home and looked over everything I could. I got some electrical contact cleaner and unplugged everywire in the engine bay and cleaned every connection (all of which looked great with nice clean copper contacts), anyway I cleaned them all and added DI-eletric grease and plugged them back in. Also I pulled the intake hose off and saw that the throttle body had quite a bit of gunk on it so I cleaned it up pretty good with some starting fluid and a rag. I also pulled and checked every fuse in the truck. Then I took it for a test drive and got really excited for a bit, lots of power! Sucks ya into the seat and everything, even broke the rear tires loose when it shifted into second! Any way as I pulled back into the driveway the rps dropped to about 100 rpm sputtered, shook and spat and came back to normal idle. Not great Idle but its ok. I will find out tomorrow on my way to work and see if the check engine light comes back on. Got my fingers crossed! Thanks for the help so far.

Alright, still runs crappy. Now I only got pending code p0135 which helps narrow It down quite a bit. That code is 02 Sensor Heater Circuit Bank 1 Sensor 1. The cause for this code for a Ford is "Engine running for 1 minute, then the PCM detected an open or short in the H02S heater circuit." So it looks like I am now looking for a break or short in the wires or something, or maybe I need a new 02 sensor? Ill dive into it again tonight.

Check all your grounds

Good to see your getting it narrowed down. Spark knock is pinging, pinging is spark knock... And it can happen for a number of reasons, but spark knock/ping is when the fuel air mixture in the combustion chamber ignites prematurely, causing that oh so wonderful valve rattle noise. Can be caused by low grade fuel in hot weather, or carbon deposits in the combustion chamber causing a "hot spot", a lean condition can also be the culprit of ping, etc, etc...

Sounds like timing chains