When structuring water with Scalar, does the temperature of the water matter? How warm can I put water on the transmitter?

No, the temperature does not matter.
As for how warm is too warm, if too hot it might cause thermal stress to the actual plastics of the coil.

For more details, please check this link:
https://www.facebook.com/groups/spooky2scalar/posts/1085496675357223/