With all codes clear I don't think you have a problem with your EGR system.
I would look at the distributor and TFI mounted ignition module. There is a Ford Technical Bulletin released, regarding a situation w/ our generation of trucks, specifically v8's, where the PIP spikes the timing every 8th firing, causing a miss.
It's a condition with how the PIP and the distributor inter-react, so replacement of the PIP alone won't cure the problem. Recommendation is to replace the Distributor ( which by doing so, replaces the PIP also). Replacement of the distributor is a lot less hassle than dealing with replacement of the PIP, so many people opt to replace the distributor as a unit anyway.
If this is the case with yours, just replacing the PIP could prove a fruitless effort. I also recommend a TFI module replacement at the same time, as it shares the same power and ground with the PIP. They also tend to share the same service life expectancy. When one goes, usually soon after the other goes.
I had the same problem with my 87 and it ended up being a bad stator/PIP. I replaced the distributor and TFI module and the problems went away.
Hope this helps