Scott,
Most small (under 15KVA) 3 phase transformers are constructed using two windings a main and a teaser with the neutral X0 point being located on the teaser winding, this is different than a typical 3 winding construction. (It is similar to the Scott-Tee which is used to generate a true 2 phase system from a 3 phase source.)
The purpose of the transformer was to provide 120VAC power to a parts cleaning machine. The existing circuit is for the control circuits and the open circuits are for future customer connections like portable tools or other ancillary equipment.
I did not check the harmonic content as I do not feel it important on a two wire circuit.
