I agree with the cummins. The 6BT like the 5.9 used in medium duty trucks and the dodge ram is darn near bulletproof. Its smaller cousin the 4BT is the same engine geometry minus two cylinders.
The older Mercedes diesels were never overly powerful, but they are very reliable.
One diesel manufacturer that caught my eye recently is MWM. They are a brazilian company recently acquired by International. They make a family of 4.2L inline sixes that range from all mechanical with a wastgate turbo, up to completely electronic with a VATN turbo.
Nissan makes a pretty good line of diesels with the newer UD trucks.
www.udtrucks.com
I've personally never dealt with them, but VW has a wide variety of diesels ranging from 1.6L fours to 2.5L inline 5 and V6, and isn't there also a V10 diesel from VW in overseas markets? I've heard mixed reports. Power and smoothness are great from what I've driven, but they say their long-term reliability isn't up to snuff.
After you've chosen a diesel, the tranny is easy. Almost any of the inline diesels you choose will either have an SAE bell pattern, or the manufacturer will make SAE adapters for it. Then you just choose an SAE transmission. For instance, the cummins has an SAE#3 bolt pattern, so with almost no modifications you could bolt up any of the Allison medium duty automatics, a Ford 4r100 or e4od from a powerstroke application, a T10 four speed, a Dana spicer 6 speed... pretty much anything that was ever installed behind medium duty diesels, or anything available today. Nissan makes 6 speeds for behind their own UD engines. Aisin makes automatics for SAE applications. The possibilities are endless