The quench isn't the distance from the top of the piston to the top of the block, it's the distance from the top of the piston to the bottom of the head. How far down the piston should be from the top of the block depends on your headgasket, and the configuration of the head, ie shaved or no. What you need to do is bolt up the head w/ gasket, and put some soft solder through each plug hole, bent in an L shape with the end touching the wall of the cylinder. Turn the engine over manually to squash the solder (one cylinder at a time using an unsquashed piece for each bore), then use some calipers or a micrometer to measure the squish. It should be in the range of 0.050, less than 0.040" and your pistons are going to be banging into the head at high rpm, a bad thing.

The piston that has less squish will have a higher compression ratio than the others, so if you were to have detonation, this would be the culprit.

Ideally you'd have the head bored on that one cylinder to match the quench with the others, and keep head cc's consistant.