The only way that the valve could kiss the piston, if you have plenty of room just baring the engine over, is if you have lost a rod bearing. That will make the clearances totally different while the engine is running. Especially since it is only on number 1 cylinder. I think that is the issue, or rather that is the only logical explanation for why only one piston would touch. It almost looks like the piston has made contact with the head on #1 as well. But, if the block was cut at an angle, you would not have so much Pto V clearance just barring the engine over.
I am sorry to be the bearer of bad news, and I hope it is something else. It is all pointing to that in my mind. Either that or the head was cut so crooked that #1 sticks out higher than the rest of the pistons.