Yes, by reading and re-reading a lot of other posts I came to the same conclusion. I bought a new muff and faced both ends parallel. I got a liner that was oversize on the o/d and turned the muff to a good interference fit and then placed under my press with a light pressure till it cooled so that there was no chance of the liner lifting clear of the liner.It might or might not be significant that the piston seems to have suffered worst at the side, not fore or aft where the valve cut outs are. One thing that became clear after a few years of the (then) new low expansion and low clearance pistons was that three to three and a half thou was not enough clearance. It might be alright if everything is correct but the base of many cylinder barrels/muffs is not perpendicular to the bore. I, and others I know, have checked several muffs and generally find that the base is off by several thou. Re-machining the base is the way to go using specially made plugs with centres to go in each end of the liner.
I also found from this that there were problems with the head recess and corrected that at the same time. This took me a while as I am not a very skilled machinist, getting better all the time.
I think that I've got it right now. I'm running 8:1 with Mk2 cams.