I mark all of my stuff.............
I marked with a paint pen the cylinder #s on the top fin adjacent to the thru-holes for the studs. Also, you can engrave the numbers on the base of the cylinder where the casting markings are located and the height groups, etc. When I had my cyl. replated by US Chrome, they took it upon themselves to stamp a 965Q inventory mark at the base area. This would be
above the base sealing surface. I don't think it's a good idea to engrave on the cylinder surface that's below the sealing surface, within the case spigot area.
For the pistons, you can engrave it on the dome/crown. If you look closely enough, you can see some stampings in the piston already.
The inner skirt area is OK too. A more solid location is the underside of the crown next to the skirt. In the picture below, it'd be the 2, 5, 7, 11 o'clock positions