You might look at the way a crankshaft grinding machine is set up. It has two special four-jaw chucks that can both be set up to hold the ends of the crank off-center so that the journals can be ground. You might be able to mount a second headstock on the tail end of the lathe and do a similar...
Do you already have a CAD system? If you are using SolidWorks, then for a middle priced CAD system I would suggest you look at Esprit, made by DP Technologies. It is a lot easier to use and learn, and of course cheaper, than the high end systems such as Unigraphics, which uses its own CAD...
A .25mm RMS (Root Mean Square) accuracy of the ideal profile is calculated from a formula in Machinery Handbook (surface texture, RMS in the index). I would think your coordinate measuring machine would be able to do this automatically, but the formula is:
RMS Avg. = sq. rt. of ((Ya2 +...
When the thread is designed, the thread flank angles, crest and root radius or other form is established, and tolerances and allowances between mating threads are determined. The pitch diameter is the point on a thread where the distance between two points on the thread flank is 1/2 the pitch...