Sorry to hear you're having problems with the valve clearances. It should be a straight forward job once all the components are removed.

Some things to consider....

Was the engine cold? it needs a good three hours to cool down as measurments should be taken cold and you will get a false reading otherwise.

Are you sure the piston is at top dead centre (tdc) and not 360 degrees out?
A good way to check this is to continue turning the engine and just after tdc the exhaust valves will start to open. If the inlet valves start to open first, you're 360 degrees out. To make sure you're turning in the correct direction put the bike on stand, in gear and turn the rear wheel in the direction of travel.

Finally double check the measurments you have for the gaps are correct.

hope this helps.....