To close the loop here, I got the engine and gearbox aligned. Using the shaft from an old beaten-up clutch we had worked well. If you don't have an old shaft, seems to me you'd have to make something similar, which is quite a machining challenge.
I got really lucky. The runout readings taken with the dial indicator on the gearbox flange face and the crankcase face (see photos) indicated the engine was sitting about 1/4" low, relative to the gearbox. I made shims out of 3/16" plate and installed them under all four engine mounts. That brought the total indicated runout down from 0.060" to 0.020". Another 0.075" under each mount brought the TIR down to 0.008", which is within spec.
I was dreading this job, but it turned out to be simpler than I thought. I suspect that is due to the factory ensuring that the gearbox mounts and the engine mounts are parallel and that simply shimming up and down will correct misalignment.
I also suspect this spec is far too conservative for those of us running Centurions today. We're more likely to do 3 miles a year rather than 3000. So wearing out clutch, crankshaft, and gearbox components is pretty unlikely.
Malcolm
