Rust spots in the cylinder

[DaveB]

I pulled the heads on the engine in my Commando to swap on some aftermarket heads and found issues in three of the cylinders. This motor has very low miles on it but it would appear that some moisture got into it at some point and left some pits on the cylinder walls. It is always garaged and never left outside, so I can only assume that I need to fog the engine when it gets stored for winter. The pits are very shallow but I presume I will need to hone out the cylinders that have issues. If I hone three of them should I hone all of them ? Would I need to re-ring the honed cylinders ?
Thoughts ?