Sprocket shaft: which shaft use to align

[ES175]

I have started to build my 1956 basket case. I purchased the parts about 6 years ago and plan on building it to be like the ones I built in the 60's and 70's. I have purchased a Santee rigid frame, springer, wheels, etc. The trans is a '36 to '64 according to the mainshaft length of 11.730". I plan on using the original chain primary and clutch. The engine is using STD gen cases, 1983 vintage. The cases are set up for Timken drive side brgs. I have two sprocket shafts in the parts box. One is 2.5" from the outside of the thrust shoulder to the end of the splines and appears to be for the roller brg set-up. The other is 2.75" long from the outside of the thrust shoulder and appears to be set up for the Timken brg. Which shaft would be used to ensure the drive sprocket aligns with the clutch sprocket? I have been reading this forum for about 2 weeks and it is goldmine of information. I used to build Harleys but after 30 years the memory dims. Need help. Thanks.

[Cotten]

We need a little more info, as your description is a little confusing.
You describe the first shaft as shouldered but for rollers
I am not aware of any shouldered shafts that were not for Timkens.
Even if you pick a '56 to '64 shaft length, there is still a question of how it will line up in the frame. The Factory changed the centerline of the motor a time or two (thus I bolted in a Knuckle to a 65-69 tranny with perfect alignment, BUT the frame was a '65 as well.)
Without a mock-up and carefull measurements, you will risk chasing your tail.