No, I haven't finished the engine yet. I bought a Myford Super 7 that needed some work to get into shape and I rebuilt my 1972 Triumph Stag which took a lot of my time away from the engine. This year I'm making a new crankshaft because the first one was 10 thou out of true on the camshaft spindle and although I tried to true it, I decided that starting again was the best way. The crankcase and front and rear parts are done, as are a lot of the smaller parts, just now waiting for the crankshaft to be finished.
Yes, the counterbore in the cylinder boss was machined after the threading. That's when I made the dummy cylinder so that I could check each bore after completion to make sure is fitted properly.
I heartily recommend the seies of articles in Model Engineer about the building of this engine. There are several useful tools and jigs mentioned in there as well as techniques to help with some of the trickier parts. The articles start in January 2002.