I'm just getting started on aligning the shaft and setting the pillow blocks. I plan on using a piece of Teflon or Delrin plastic for the large spacer (approx. .380" thick) under the front pillow block bearing and thinner anodized aluminum shims under the remaining bearings.
McMaster Carr sells the alum. shim kits - (10) 6" long shims of various thickness. I had thought about using laminated aluminum or laminated stainless shim stock but I'll see how these work first. The laminated shims are nice to use because you can peel off the layers to get just the right thickness. The layers are usually .002 - .004" thick and the shim stock is available usually up to 1/8" thick.
The construction manual calls for aligning the shaft using wire, an inside micrometer, pulleys, battery and a small speaker. I'm assuming the manual was written before inexpensive laser levels were introduced. I've done some trial runs with a Craftsman laser level and a camera tripod and it looks real promising. I'll detail it in the log later if it works.