I have a 1999 Dakota that came originally with a 3.9 5 speed. I bought it from a guy, who bought it from a guy, but I'm actually looking to put some time and money in this thing but still on somewhat of a budget.

I'm not sure, but I'd say that the seller was not telling the truth by saying it had a 318 tranny bolted behind it. I'd say I think its the stock 3.9 tranny and t-case even though he claimed that he used a ram transfer case.

The motor that's in it, from all I can tell is a fuel injected 360 with headers.

What years/models transmissions can I bolt behind this motor?

 

If it's an NV3500/NP231D, it's fine as-is. The transfer case should have an ID plate on the back that will tell you what it is. For the transmission, Google pictures of an NV3500 and see if it looks the same.

*EDIT*
Here, I saved you the trouble.