John,
Man...I'd start at the beginning again with checking for fuel line leaks. Pull off the forward splash pans and see if you get any weeping on the ground after it sits overnight. The volume of air leaking into the system is a higher % at lower rpm/idle fuel delivery causing more noticible rough running. At higher rpm the volume of fuel being delivered is significantly more than the bit of air getting into the system so it may seem to be running OK at speed but it will still be leaking. You should be able to smell fuel when you pop the hood in the morning if the lines are weeping. It does not take much of a leak to through off low idle speed.
Good luck

__________________
FRED

Daily Driver: 98 E300TD 199K
Hobby Car: 69 Austin Mini
Past Diesels: 84 300SD, 312K
87 300SDL, 251K
94 Chev. K-1500 6.5Ltr.TD, 373K