I asked my transmission builder which yoke I should use before the transmission arrived; they said any slip yoke would work. I bought a Spicer 3-3-5551X.

It looks like the builder used a fixed yoke output shaft, and the spicer yoke is one of the long units. The yoke obviously engages the splines fully and will bottom out past the splines if allowed to (a shorter driveshaft will obviously prevent this).
My main question is, should I be running a shorter slip yoke? I can't think of any immediate issues with having the yoke stick out as much as it is so long as it's fully engaged. What do y'all think?

 

Absolutely run a shorter slip yoke. I wouldn't want to take that chance it might somehow get jammed up and destroying my transmission

 

The shorter yoke will lessen the chance of vibration for sure. optionally you can have the yoke you have cut . You certainly though must have some movment area .
The shaft looks like was cut on lathe just not far enough up. nothing worng with doing that.