MarkT really a great write up!!!  

Rectifier normaly mounts up under the tank around the coil area .
& now i've said that i can't find a pic to prove it.
Looking at the parts pic i forgot early models had a different rectifier mounted somewhere else but i guess you're using the common more modern type & think it might hang under the frame bar below the coil.

www.partzilla.com/catalog/yamaha/motorcy...3/electrical-ct2-ct3

On my Ct1c it attaches to the battery box 

Yep think it is too on my AT1 magneto model come to think.
So if your new loom is for a CT1 the wiring might expect you to hang it somewhere under the battery box & if you find a CT1 box it might have a mount under it for that, but for the early type rectifier although probably easy to mount a modern one there too.
Original was a fin type for cooling but doubt it matters.
Where ones i'm thinking of mount under the tank is right above the motor so doubt cooling has a lot to do with it. More like heating under the tank.