I take it this is the incomplete engine in your other post?

If both cylinders are to be the same bore, it is not really a compound.

For 1/2 inch bore the piston length could perhaps be anything from 1/4 to 1/2 or a bit longer, depending on how you intend to seal it – for a low working pressure you could make it long, and just put some oil grooves in.

Clearances are not going to be critical on something like that – aim for 1/32 each end, but 1/16 will not hurt.

Since you have the original valve gear, I would work out the valve travel and port face dimensions alongside designing the cylinder, and this should give you a few clues to the original proportions.

Mill engines usually had quite long cylinders, and bear in mind the rear cover needs to be fairly long to accommodate the gland.

It looks quite lightly built, so do not try and extract too much power from it!

Just my opinion.

Here is the Bassett Lowke replica I did last year

12mm bore 0.75mm voids, 0.75mm cover spigots, 6mm piston thickness with 2 oil grooves only thing different is the stroke was shorter as it's a high speed engine

It's possible that the spigots you have may not have been to the cylinder bore, it was quite common to have a cylinder cover and then the flange of the engine frame so your spigot could have gone into a female hole in the rear cover which would have had a male spigot on the other side sized to suit the cylinder.