I took my wheel off to change the tyres and removed the calliper so to get the wheel off.

After changing the tyre and putting it all back together I am finding that the throttle side disc is grinding on the outside face on the top 2mm of the disc. The clutch side brake is perfectly ok. The brake slider pins are working ok as well.

I cannot see anything obvious that is grinding so must be missing something obvious. Is there a 'special way' to mount the front wheel and align the brakes up?

Just a thought... You did put your wheel in the right way round? Although it doesn't look like it at first glance, the hub is not symmetrical along its centre line.

Did you bounce the forks before tightening the pinch bolts to centre things up?

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Loosen the pinch bolts and axle.
Sit on your bike, pull on the front brake and bounce the forks up and down a couple of times to realign the forks.

Tighten up, and should be good.

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Bike: 2013 XT660Z, TKC70 tyres

Mods:
Barkbusters, Scottoiler, DIY Tail Mod, DNA Stage 3, Power Commander V & O2 Eliminator, Exan X-Black Stainless exhaust, Tool tube, Ohlins linear front fork springs, Nitron rear shock, JT front and Supersprox rear sprockets, D.I.D. VX 520 chain, Adventure Spec bashplate, DIY USB Outlet, DIY chain guide, Kev's Throttle mod

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Pleiades, yup wheel is correct with the flanged spacer on the clutch side.

I hadn't thought about bouncing forks up and down with loose axle and pinch bolts so will give this a try to see if it sorts it out.

Thanks to everyone for their help.

Have you got a pad on each side of the disc? Steve.