The machine completes one product every 6 tape loops. Here is what it does on each tape loop:

Loop 1: Grab an input. If the missing bond is between water and earth, the nucleon is sent through the conduit.

Loop 2: If the missing bond is between fire and earth, the nucleon is sent through the conduit.

Loop 3: If the missing bond is between fire and water, the nucleon is sent through the conduit. Drop an output.

Loops 4-6: NOTHING MEANINGFUL. Arm 5 could have been a biarm, but the secondary is gold, not cycles.

The hex arms will reassemble the nucleon in the same way, no matter what - arm 1 moves the two "cherries", and arm 2 handles the single "stem". However, the earlier the nucleon passes through the conduit, the more it gets rotated by arm 3 before getting outputted by arm 4.

On the input side, the nucleon is presented to arm 6 - if both cherries are next to it, then the nucleon is sent through. Otherwise, the nucleon is reconstructed as needed and rotated.

The key here is that the nucleon is rotated 120 degrees each tape loop, no matter which chamber it's in.