How do I measure a small piston to head clearance

[Brian]

Mate...ring me. Sorry those heads I sold you are giving you grief. I have the tooling to sort it.
Your technique of fitting heads sans gaskets and checking clearance is spot on! It's what I do. I have struck your problem before, I made a tool that exactly replicated the radius of a Ross piston, [I have another that matches Ford piston] and have a fixture to hold head in milling machine in order I can machine whatever needs to come out.
You need to determine this amount for each cylinder. Don't bother with clay etc, you already know you have contact, so that ain't gonna show you f@%$ all! Use either feeler gauges or a DTI to determine how much the head is lifting as each piston comes up and passes TDC. Write these amounts down. Also, take note of which head fits which side, although, in theory it shouldn't matter.
Send the heads and your information to me and I'll machine to suit.
You can do it like others have described above, but by using a form tool with the correct radius, the contact points are the bits that get machined off, no need to use playdough etc to show where.
Now....if its the valves that are hitting, its a different story. I have no fancy tooling for that, I just use a die grinder and carbide burrs.