Wow a foot+ long shaft, now that's got to be a big engine.
Is it a two piece hollow shaft?
Just leave all the balancing for the last steps in making your turbine. Get all individual parts balanced reasonably close then balance everything as a complete unit, turbine wheel, compressor, shaft, nuts, etc.
I got all my work done at a turbo place as they had all the expensive balancing gear. final balancing was performed with the turbine assembled with diffuser and rear cone removed.
Go and have a chat with a few of your local turbo builders and tell them what your doing and ask how you should go about it.
These guys balance parts that are turning in excess of 200,000 rpm daily so most of them really know there stuff. My engine was balanced for $50US.
Not really worth stuffing about.
But you might find this interesting if you are really keen.