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Yes, the only option that will not work on your truck is the transmission tuning, which is an additional $40. You can still purchase the trans tuning for your truck from Superchips with your VIN provided. You don't need it though, the programmer will work just fine on your truck without it.
This. ^^
I purchased the trans tuning option on mine and believe me, it is more trouble than it's worth if you don't know what your doing. You can really screw up the transmission. There is a thread in the 3rd gen Dakota section on the trans tuning option, describing how it is accomplished, with spreadsheets, etc. Honestly, Dakotaff is correct, the canned tunes are more than adequate. You don't need the trans option unless you really want to dig into the inner workings of the transmission tuning.
This is a GREAT price for this tuner. A lot of people on the facebook page who never check the forum would be interested in this. If it were me, I'd link this page in a post on the fb group page.