I would like to know if the out-put splines on the trans and the in-put splines on the TC are the same.

Maybe.  What vehicle are you asking about?  2wd or 4wd tranny?

oops  sorry That would most likely be needed.
It's an 88.5 Sammy 4x4.  I am putting a Mazda 2.2 diesel and 5speed trans in,  and am thinking about the transfer case connection.  I have to move the TC back 3" and want the shaft as short and possible.  If the splines are the same I may try two slip joints with a universal.  

jerry

Just cut and shorten the samurai intermediate shaft.  You can shorten it so that the 2 ujoints are practically back to back, which makes it considerably shorter than what it is now.

The samurai tranny output shaft and the samurai tcase input shaft have different spline counts.

If you are asking about a mazda 5 speed tranny output shaft spline count, then I have no idea if the mazda spline count matches the samurai tcase input shaft spline count.  The samurai tcase input shaft has 26 splines.

sorry, But I would love to have a picture of this when you get the two slip yokes on there.Skyhiranger  you have way too much patience! Lol.

Here is what a stock intermediate shaft looks like once it is shortened.  This is the shortest that it can be made, by cutting out the tube and butting the 2 ujoints together. 
I suppose you could shorten it up even more, by grinding the ujoints, but squaring everything up might be an issue, if you do that.
You could also just use 1 ujoint in the shaft, but unless the tranny and tcase is perfectly aligned and braced so that they never change their relationship to each other, I would be worried about driveshaft vibrations.
I would not try to run a double ended slip yoke driveshaft.  For one, I see no benefit in it.  For two, you aren't really going to be able to make the shaft any shorter than if you just ran a flange on the samurai tcase.