"Big Picture" approach to looking at diagnostic codes?

You forgot to mention mileage, engine type and any drivability concerns - all useful information to diagnose the problem(s). It's unlikely that all these codes appeared at once -- have you been driving with the CEL on for quite some time?

Hopefully one of the pros who frequent this group will soon chime in. In the meantime, if you want my 2 cents: a) The misfire on cylinder 4 is very likely related to the codes on the relevant bank. Can't tell whether 1 or 2 -- we don't know if it's a V6 or a V8. I would start with fixing it. Take a good look at the plug in that cylinder and compare it to the others -- there will be good clues there. A faulty injector, a stuck valve, etc is possible, but ignition would be my primary suspect. If the spark plug wires have not been replaced over the last 30 thousand miles, I would do that, even as a precaution - they don't last much longer than that. With any luck, that may cure the other bank's problems as well. b) The most common code for that EGR-related code is a defective DPFE sensor. It's fairly easy to test, but if you don't have the tools or the knowledge, the part is cheap and easy to replace. I believe that there was an 'extended warranty' issued due to its premature failures, so you may get this done for free.

It is important to differentiate between codes that are "causal" and codes that are "symptomatic".... Putting it as easy as I can, many concerns can generate multiple codes.... a misfire can generate lean codes since misfires will increase the amount of unreacted oxygen in the exhaust. A lean system can generate misfires along with misfire codes. And on and on it can go....

Now, I am having to assume that these codes are continuous memory codes but I can't assume anything about the capabilities of your code reader. In the shop, I would have performed the KOEO On Demand test to retrieve the DTCs. If any of these codes had been returned as an On Demand or "hard" fault, we would address these before moving on.... If none of these codes appeared as "hard" faults and were only present in continuous memory, we would run the KOER test - there are many actuators and sensors that the PCM cannot test without having the engine run.... KOEO continuous memory codes have the possibility of being hard codes during the KOER test.... Again, hard codes are addressed first.

If our scan tool doesn't offer us the ability to perform these two tests, the only option left is to note the existing codes and then clear continuous memory... drive the vehicle and see what returns first.

Since your post is totally bereft of any essential information, I can't offer any more advice than this.

Jim - I was concentrating on the concept, not expecting a diagnosis; however if you wanna take a swing at it: 200,000 miles on a 6-cyl,

Oh, and plugs and wires replace within last 5,000 mi. - Mike

Oddly enough, you are still keeping some important information secret - like whether it's the pushrod or the overhead cam 4.0L. The latter had its share of problems, including, if memory serves, a notorious intake manifold vacuum leak. At 200K, those have probably been repaired a long time ago, but who knows -- you told us nothing about this vehicle's history.

Jim Warman is the uncontested expert on this group and an overall great guy. Heed his advice about running on-demand diagnostics and servicing those, starting with the first code that shows up. Hopefully you have the Power Train Controls/ Emissions Diagnostics Manual - follow the charts there.

I'm gonna hang my ass way out in the breeze and opine that you will find there is probably a DPFE in your future.... In the late 90s Ford had (IIRC) three different flavours of intake manifolds on the OHC engines.... I'm not sure if any of these featured ported EGR flow - this is something to consider in regards to the cylinder #4 misfire.

Which ever way, smart money is on repairing any conditions that can be proven and then re-evaluating.

Michael, this group has amateurs who play with cars in their spare time when they are not amusing themselves with something else (like me), and very few high caliber, experienced pros (like Jim Warman). We all deeply appreciate the latter group contributing their time here for free, when they could be making oodles of money for themselves or for their employers instead. To help them help you quickly and efficiently, put yourself in their place. They can't see or hear your vehicle and don't know its history, so you have to provide it here. When you have a problem with an engine, you have to say what engine it is, how it has been maintained, how many miles; and provide the best description of the problem and what have you done so far to resolve it, not just a snippet of what your code reader extricated out of the computer's memory. Makes sense, doesn't it?

My Expy has the 5.0L engine, so I can't contribute anything from my experience about your 4.0L SOHC. In its early days your engine had a whole bunch of problems like faulty intake manifold and timing components. If those have not been taken care of, it's probably a good idea to google the archives of this group for symptoms and solutions to those. Otherwise there are no miracles: systematic troubleshooting will get you to the root cause, and the Power Train Controls/Emissions Diagnostics Manual will provide that in great detail. With an engine that has already served 200K, I would not ignore what that manual calls "Base Engine" - mechanical issues related to the engine itself. Get a good look at the plugs, comparing the one in the misfiring cylinder to the others. If you don't know how to 'read' plugs, learn that - the information is available everywhere. A leakdown test is ideal, but a simple compression test will also point you to a major problem in that cylinder, like a stuck valve or piston rings that are not sealing.

The code for insufficient EGR flow seems to be an easy target. If that's consistent, repairing it may address some of the other issues. The most common cause is a faulty DPFE sensor, but it could be a clogged hose, bad solenoid, etc, etc. The same manual will guide you through the systematic diagnostics if you are not a gambler.

Some will question the wisdom of all the time and expense of doing this on your own -- or even of doing this at all, instead of dumping the 10-year old vehicle and buying something newer. I don't have a good answer. Except perhaps that my 22-year old, throttle-body injected LTD still passes emissions with flying colors (anybody knows a source of replacement window sweeps?).