The advice to keep away from AC and cross at 90° where ever possible, is sound advice.
Try to do it that way, as best you can. Can you keep them at opposite sides of the joist bay?
Possibly add a few 2 x 4 studs as a shield between the two types of wires in the bay.
Are your speaker wires going through the same hole as your AC wires?
Most of the time, a zones 2 and 3 aren't critical listen areas anyway, so give it a shot. From your description, it sounds like options are limited.
To answer your second question:
No, you cannot mix high and low voltage in the same J-box. It's against code.
Though they do make boxes with approved dividers. There is a possible noise issue though.