Scott, One point made already sort of is the emissions stuff. Depending on where you live you will need to get it checked. It can have an aftermarket exhaust on it but has to have the "diesel cat" on it. Check to see if the EGR plumbing is there and ask if they removed the heater grate, a big mode on the 5.9 and 6.7 motors. As far as the transmissions go they are strong but any brand can break after 40K because of driver neglect/abuse.
I owned a 07.5 Dodge for 4 years till I rolled it coming back from CM one mile from my house. I was planning on keeping that truck till it was not needed anymore and then maybe even longer. Dodges do fall apart easier and aren't as tight put together than the Fords and Chevy's. I searched 4 years ago for a Chevy because I liked them then Randy and I took his Dodge to Moab and I was sold. I now have a Chevy Dually and am not as happy with it as I was with my Dodge.
The perfect truck in the diesel community for a lot of people is a Ford body, Dodge 5.9 motor and an Allison transmission. Sounded like you already know that and have thought about it.
BOT Look at the steering box, known for leaking. Check for the Death wobble also known issue and has a $200 fix. Radiators, the fins are easily "dented" for a lack of a better word and can cause cooling issues over time. If an aftermarket filter is being used check the MAF and the tubes etc. Programmers are OK BUT!!! If there is one on there ask him or her to see it (if it is a plug in style i.e. H&S or Smarty most likely) have him plug it in and then check to see what setting it is on. On the Smarty anything above 4-5 and they were only after the power. Gauges are very important! The most important one is the EGT or Pyro. Exhaust gas temperature is a Diesels biggest enemy, each brand is different and so are the temps that people will tell you. I have had my Dodge up to 1850 * for about 5 seconds to pass a car that cut me off and then slowed down up the tunnel pass. If there is an electronic gauge system used like an Edge unit or Banks you can look in the memory bank if they have not erased it. Go through the menu and check the memory, it will tell what his top speed was, highest EGT, Trans temp etc. you get the idea. Some plug in programmers will also do that when you scroll through the menu of them.
Besides those things I think you have most stuff covered. Here is a great website that helped me a ton http://www.cumminsforum.com/forum/
Good luck and if you have questions you can contact me at 3o3....829///o7o3 and am more than willing to help you.