Have you seen
this thread about a lot of bad fuel going around lately?
Im having similar symptoms that came on all of a sudden. (lots of smoke and a clanky nailing sound at idle)
I have been reading around the forum the last few days and there does seem to be a lot of threads with similar symptoms.
I am currently working on eliminating the possibility that it is bad fuel before I move on to thinking I have a more serious engine problem.
I re-did the valves and changed my primary fuel filter that is a big goldenrod bowl type. There was a lot of grey chunks around the bottom that looks like moisture in the fuel.
Also got some fuel from a bigger higher volume station and added a strong dose of PowerService cetane additive.
That made some improvement but the same symptoms are still there.
Im heading out now to get some DieselPurge and a new spin on fuel filter. I will report back if I have any success with that.