I am in the process of integrating the HPV shell design program from Recumbents.com, a CFD program, and the Pepakura paper model software to make skin for my fairings.
I am not real handy with links but go to the recumbent.com Forum section and select Technical / Bike Building. There is a thread on the HPV shell design. The software has provision for upright bikes as well. There is a separate thread for upright bikes. Typically a TT bike is 7/8 the size of a motorcycle. There are several CFD programs available. The Fluids6 and Autodesk use .stl files and these work (supposedly) with Perakura Design for paper models. I am just getting familiar with each.