Hey! I am new to Dakotas and Mopar but I have looked into this quite a bit before buying mine. Its never super easy to do a manual swap but a Dakota doesn't seem that bad, just make sure you get all the components to match the chassis configuration. I.e, quad cab 4x4 etc. You need to match the years pretty good though, I believe they change a few times around the early 00's. Ralph laid out the basic list above.
Need to add the clutch actuation though, I am not sure yet (just got my Dakota) if we have a hydraulic system or not, I am assuming we do. You will need to acquire and mount the reservoir, lines and master cylinder.
The transmissions for 4x4 and RWD are different on account of transfer case. You will need to match the front (4x4) and rear drive shafts to chassis configuration.
The K member will be different too. Will probably need to do something with the console where the shifter will go.
Hope this is at least a start for what its worth.