Steven Sesselmann wrote: How do they measure ion energies?

Steven

From the spread in neutron flight times.

A D-D fusion reaction always releases neutrons with fixed energy (ie. velocity). But this velocity is in the centre of mass frame of the two fusing deuterium ions. So the actual velocity of the neutrons will be spread by the thermal velocity of the ions, ie. whether they were going towards or away from the detector at the time.

Since you know the distance the detector is away you can find the velocity from the flight time. The shape of the velocity curve should be roughly Maxwellian, so by fitting a curve to it you get the equivalent temperature.