Okay I have been looking to swap out my 239 3.9 v6 magnum in my 99 sport base and I was wondering if I'm able to put in a 318 v8 magnum from another dakota . am I gonna run into any problems with bolt alignments on the tranny or what ?

 

Yes a 5.2 will fit. The transmission will bolt up but it won't last if you beat on it.
The basic dimensions are the same between the 3.9 and 5.2 and many parts, such as the water pump will bolt up.

You'll need a PCM and have to either add the two extra injector wires or get a harness from a 5.2/5.9 - from a '99 Dakota.