Put the leg on the towel, the foot will then be able to move in a larger ROM. The towel goes on the lower part of the leg. Do not press the insertion of the Achilles tendon with the towel.

To increase range of motion a towel, or any item create a small amount of knee flexion, would need to be posterior/underneath the knee, not at the lower point of the leg. The rationale is that the gastrocnemius is biarticular, so reducing the proximal muscle fibre length provides greater opportunity for fibre length increases distally during dorsiflexion.

A metronome is a good idea to standardise the movement. If you pick a set point at which there is a rest period this will help track the position and allow a brief rest period for re-perfusion - for example one beat on a metronome.

The tricky point with the situation you describe is where should the set point be? If you pick maximum plantar or dorsiflexion, a muscle contraction will be required to hold the position. If you have a rest stage in a neutral position how will you standardise the exact position? I suppose you could go old school and set up some string which would lightly touch the tip of the participants toes to provide feedback about what the rest position should be. Likewise, you could also position string at maximum ranges of motion.

It would be interesting to know whether you are looking at plantar flexors, dorsiflexors or both, though the above suggestions are fairly broad and applicable to both.

The only real way to assess reproducibility/reliability is to complete multiple assessments on the participants and statistically analyse them once you have standardised the protocol as much as possible.

Hope that helps.

Dan