I was given this info on another very informative forum you may want to check out carolinak5.com
Anyways to tell whether or not that JY np208 you are looking at is for auto or manual tranny
1. Passenger or driver's side drop for the front drive shaft. Self explanatory.
Auto is on drivers side
2. On the back of the case is a dial disc, that has the pertinent information on the t-case. You want a 208 "C" as this is the only t-case that will work properly.
If the case is marked 208 D, F, or J you cannot use it.
3. Lastly, count the spline on the input gear. This may not matter since you are going to rebuild it and you have yours at home, however, having a spare is nice, just in case. They come in two varieties: 27 spline and 32 spline.
27 found on TH350 and 700R4
32 found on TH400 and SM465
Some PDFs on rebuilding the cases and other general info.
Hope this helps another noob