Well guys, I put about 150 miles on the 6.0 yesterday. Everything was great, got right around 20 mpg with the Looney tune. Later that evening I took it to the local softball games, about 10 mile drive one way. Upon arrival I hinted a very slight miss, but decided I was hearing things. On the drive home, I found I hadn't been hearing things, the miss progressively got worse, and it developed a shake at lower RPM; made it home but died when I let it idle.
This morning I started diagnosing. I had a new set of Motorcraft fuel filters, was going to put them in about 1,500 miles from now as it will be time to do the oil as well. Decided that would be my first step. It started, but barely and ran same as it had been across the yard to the shop. Shaking at lower RPM and blips of the throttle resulted in loads of black smoke. Changed the filters and no change. Old ones were a little dark, but nothing alarming. I changed the tune back to stock, still no change. Never had a check engine, but checked the CTS and it had a code for cylinder 5 contribution.
Next i tried unplugging the ICP sensor and letting it run. I still detected a slight miss, but it started and idled nicely and the shaking was gone. Plugged back in it seemed the same as unplugged. CTS showed the low ICP voltage code, cylinder 5, and 1 contribution. Cleared those and took it for a drive. Stock tuning it seemed to be running pretty much like it should, but was smoking excessively. Smoke on stock tuning was comparable to what the looney tune did before it started acting up. Once back in the yard it had thrown the cylinder 5 code again.
Last thing I tried was unplugging the ficm and inspecting the connections. All looked good so I put it all back together and cleared the codes and went for another drive. The miss seems gone, and it is running nicely, but it is still smoking more than it should on the stock tuning. Return to the yard and it hadn't thrown any codes. Turbo was cleaned somewhat recently, would make about 27 pounds at WOT so it's getting boost.
Other things to note, FICM is always monitored and has never dropped below 48 that I have seen and it never threw a CEL through my testing.
Sorry for being long winded, but I've run out of ideas. Do I have an injector on the way out, screwy FICM, fuel PSI troubles (no guage for that at the moment, but am running the blue spring)? It was throwing the cylinder 5 contribution code pretty regular, number 1 only came up once.