Ok. here are the problem parts.
Hayes 9 hydro brakes
DT swiss hub (but branded under hayes???)
Fox F100R (roughly 2003-5ish)

the rotor is way out of line, it is way to far to the spoke side of caliper, this is with the calliper pushed as far as possible across the post mounts as possible, the rotor is rubbing agains the brake (and even erroding some of the calliper as it goes :o). I can't think of a way to fix it other that putting some fine washers in between the rotor and the IS mounts, is that OK? or is there some thing more obvious that I am missing.

I can only think that this is a problem with my hub surely both Hayes and Fox know what they are doing, and have got their machining down to a tee?

thank you.

Assuming everything else is set up as it should be then these might be what you want? Or fine washers.

Longer bolts for the mount/caliper and space with washers.

It is vaguely possible that the tollerances on all three parts could be out to the point where the caliper and disc are touching. There could also be a problem with the brake mount adaptor.

There's also a chance that the fork has been over "faced", so that the caliper is now sitting too far out (left).

Assuming that everything is assembled correctly, you can sort it by either shimming the mount adaptor with paper spacers, and/or shimming the disc with rotor spacers.

the rotor is way out of line

those spacers look useful but 8 is still only 1.6mm 🙁 I think spacers on the post mounts would be simpler…

If it is a post mount fork can you space it? Only if it is a post mount adaptor?
So, what is it? 🙂

I would have thought with a"Fox F100R (roughly 2003-5ish)" it would be IS mounts on the fork, with a postmount adaptor.
I'd space the adaptor from the fork. Easy 🙂

I'd agree with PP. A 2003-5 Fox fork would be IS. Therefore, I'd have to assume there was an adaptor between the fork mounts and the caliper. Use a few shim washers to move the adaptor over as you would with any IS set up.