Lincoln has bupkis for a dedicated diesel shop that works on trucks. Theres like 3 places I know of that'll work on commercial vehicles. So when you see diesel in the yellow pages, that's what youre getting. The Int'l dealer on Cornhusker says they'll work on the Intl engines, but I havent tried them.
Matt at Anderson Ford is a pretty good diesel guy. Its a dealership, but he wont screw up your truck, or you in the process. Randy Wermuth at Diesel Specialties of Omaha sounds like more of the kind of shop you want, but its Omaha. 132nd and . . . I forget. North of W Center about 6 blocks.
Just general really good shop is Trade Center Auto, but they're not diesel specialists, so they'd bow out of engine work, but they'd do anything else (suspension, tranny . . . etc)