A couple of considerations:
1 – Shafts are rotated independently.
2 – Use the inclinometers (outside two numbers) to match angles within less than .5 degrees before taking a measurement.
3 – The shafts might roll due to the weight of the sensors. Instead of trying to hold them, use a steady rest to hold the sensors in place in the horizontal plane. A dial indicator base with an adjustable arm and rods work great for this.
4 – Use the Verti-Zontal process to complete the alignment.