I guess you have split your other tractor before, you said on page 1 of this post.
If you haven't split a Cub at the rear before, I'm thinking you might want to split it at the rear of the engine first, like you said before.
If you split it at the rear, both housings have to be held so the front of the shaft doesn't move up or down.
Also, if you split it at the rear, when you put it together, the front of the shaft has to go through the hole in the throwout bearing, and into the clutch disc.
You can decide which way you would rather split it, I don't know how many tractors you have repaired, or what equipment for splitting you have.
If you do a rear split, don't push the clutch pedal down when it is split, the clutch disc would fall down out of position.
Below is the Cub and LoBoy service manual, it has lots of info.
There is a contents beginning on page 1 of most sections.
I would read section 4, about splitting the Cub.

http://farmallcub.com/rudi_cub/www.clea ... index.html