After some conversations with Charles and the comments from Henry, I have downgraded the apparent "damage" on some of these cylinders to be not so terrible. So now I will measure them and see if the Piston to Cylinder clearance is acceptable.
Charles provided this procedure that I plan to follow (thanks!!, posted with permission):
Assuming you know the diameter of the pistons and they are all the same since they are new, here's the way I like to measure cylinders.
You will need a table to collect measurements. I like using a digital precision dial bore gauge; I have one that reads in .0001" increments for this. You will want to orient the cylinder such that it is sitting how it would go on the engine. Picture 0 degrees as the top of the cylinder that points towards the heavens. Then also imagine a point 90 degrees clockwise from this point. You will be taking diameter measurements across the bore at 0 and 180, 90 and 270. To be even more thorough you can measure across at 45 and 225 degrees too.
I then measure at .800" down from the top (top being the surface that mates with the head), 1/2 way down the bore (not including the skirt of the cylinder- head to deck length of the cylinder only), and at the start of the skirt (right around the point where the ledge that rests against the case is). You will want to take each measurement such that it is repeatable within .0001". No more than .001" of taper from top to bottom is allowed, as long as the bore remains in spec with regards to total piston to cylinder clearance. No more than .0005" of ovality at any given point within reason, although I do like them to have little or no ovality towards the top (that's why I measure at .800") where the rings will be doing most of their work.
This is hard to nail down because it highly depends on who is doing the honing, the condition of the diamond stones, how many stones are used, honing pressure, etc. There is no such thing as a perfect bore. I have had customers searching for that perfect cylinder who go through the trouble of CMM'ing cylinders and it is possible, but it takes lots of time and $$$.
Another good measure of how square the cylinder was after being remachined (if top deck and cylinder bases are parallel) would be to measure the head to deck length of the cylinder at the four corners (45, 135, 225, and 315 degrees). It's hard to say what is right or wrong other than we shoot for the no more .0002" difference between measurements, although I would guess that anything +/- .0005" is as good as new.
Another measure is the perpendicularity of the bore to the decks, but this is almost impossible to measure statically. We have a special mandrel that centers on the bore across the entire length of the cylinder which we then can freely rotate the cylinder and use a dial gauge traveling across the top deck to do this measurement. Again, we aim for no more than .0002" difference but anything +/- .0005" is as good as new.
All measurements should be taken at ambient 65 degrees give or take a degree or two and all measuring equipment should be at the same temperature. Measuring tools will change their readings as they get warmer, do be aware that if you hold your measuring tools too long it will change readings as much as .0005". The same can be said of the cylinder base that rests against the case, although this is harder to measure.
Before taking any measurements I am careful to clean all tools and the cylinders thoroughly, and I lubricate the bores with a quick wipe of non-detergent 30 wt oil, but any oil will do.
This takes me about an hour to do to a set of six cylinders, and I do it all the time. Be patient and i'm sure you'll be able to do it.
Charles L Navarro
LN Engineering
http://www.lnengineering.com
Aircooled Precision Performance