These trucks came stock with the short shaft, so if you were to grab a short shaft Th350, then you could possably save a few bucks on drive shaft modifications by getting a strock th350 equipped drive shaft(s)
However, other than the drive shaft, there is no reason to not get the long tailshaft version. They are more common, and if you are thinking of a one piece drive shaft, this will shave off a few inches which can make it a $200 ordeal instead of $500.
Your parts list does look to be about right. The pedal assembly doesn't need chainged...the assembly is actually the same from one to the other, the only difference is the clutch pedal is removed for the automatic driven truck.
you may or may not need a new speedo cable too...small detail, yet makes going through the local speed trap much less nerve wrecking.