It does have the rubber bushing under the large washer plate. I didn't see any visible issues. Should I be getting no resistance if I measured the two red wires? I'm getting 4.6The toroidal transformer appears correctly mounted (using a mounting kit) with damping material beneath the top securing plate. Having the connecting wires at the mounting surface is normal practice – I very much doubt over tightening of the securing bolt has squashed the wires, causing the issue, since the enclosure is made of plastic.
All the toroidal transformers I’ve seen are wound with the secondary wires wound above the primary wires on the toroid. Personally I think there is likely a short within the transformer (either in the primary winding or one of the secondary’s) – which will need replacing. Once you remove the transformer, there may be an indication of the damage location.
If you are lucky there will be a rating label on the transformer side wall listing the electrical ratings (input voltage, with each secondary output voltage and current rating) – if you are even luckier, you will find a replacement transformer having the required input voltage and secondaries.