It was an interesting and eye-opening (for me) quick test - I've learnt from it so all is good for me. Don't blame Jazz re. the mounting method - that's how industry does it - single bolt through the grounded chassis. As Clive says the two rubber sheets are a form of mechanical protection to allow you to positively clamp on the transformer windings without deformation of the windings and compromising the insulation coating on those windings. The sequence is chassis (bottom) -> neoprene washer -> toroidal transformer -> neoprene washer -> steel plate -> nut.

Re. colours - that's a less than useful label on the transformer but I'd interpret it the same as you say - positional reference indicating the phase of the windings. I've had a quick look on Airlink's website and there's no further useful information that I could spot. Your fuse will tell you if it's wrong.

I've missed the earlier conversation on this but guess you're using AC to power the stepper drivers (no sign of provisioning for rectifier and caps) - I'd think carefully at this time of routing the secondaries in a tidy(!) route away from any low-level signalling, to the drivers - I'm sure you're looking to route to the top of the picture of the box.