Michael,
I rebuild Model A and B engines. For an engine that is built for standard service, I hone the cylinders to provide a minimum of .0035" clearance. If the engine is to be used as a touring engine and will see duty under prolonged runs at higher speeds, I hone to .004" clearance. I also slightly increase the clearance on #3 and #4 cylinders as, from my experience, I think they are a bit more prone to scoring. 2 tenths of a thousandths is sufficient increase for these two rear cylinders.
Good Day!
Dave in MN
www.durableperformance.net