You should do tower flyby's with the cone in order to calibrate it at whatever trail length you're going to use. In my insignificant experience, the trail length variation is inconclusive so you're probably not going to use it as a calibration parameter.
When I was involved in air data and RVSM certification we certainly calibrated the cone installation using tower fly-bys. We used a constant pipe length (and trail length) regardless of aircraft series and the calibration was usually the same. The overall pipe length being the variable rather than trail length.
All the info you need can be found here.
spaceagecontrol.com : Main > Data Sheet - 100101 Trailing Cone
We designed our own but that looks familiar.