Some turboprop engines have a two piece driveshaft, (Inner, main shaft transmits the torque, the outer is a floating reference sleeve, locked to the inner shaft at the input end.) and use phase shift between the two shafts as measured via gear type pickups at the output end. So long as you know the modulus of elasticity of the inner shaft, the phase shift is a rock solid method of torque measurement. Allison uses this system on their T56/501 engine line, to give the pilot a torque reading for each engine. (C130/L100 aircraft.)
Not sure if this can be adapted to your particular application, but if you have a single output shaft transmitting the torque, it may be suitable. (And parts are readliy available, cheap.) We've used this system with optical pickups as well to measure the phase shift, which promised to be simpler, however any dirt or oil covering the optical strips caused grief.
Robin Sipe.