How does one determine the freestream and ultimate slipstream velocities to estimate thrust?
The free stream velocity can be measured with a calibrated air data system. This uses a pitot tube somewhere at the front, the readings of which have been compared to known speeds in previous flights. The difference between the total pressure and the static pressure gives the dynamic pressure which can be translated into the desired speed.

The speed in the slipstream must be measured across the full cross section to ensure that the full speed profile is known so the slipstream speed used for thrust calculation really is the mean of all the speeds in the slipstream. This is done by measuring the total pressure at several locations, for example by using a moveable rake.



Combined temperature and pressure rake (picture source)