I have been aware of "drunk" bores relative to the base cylinder face elsewhere so when I came to finish the two new sets of B-Rap cylinders that I got 30 years ago from the Spares Co I checked them and found same faults too. Cure: I set them up in the lathe gripped with the three jaw from the head side and checked for runout as deep inside as the clock was readable plus same check at the bottom end. My three jaw chucks resp. the mounting plates for the lathe are all relieved by one millimeter play to be able to get any workpiece into good runout position via tapping the chuck with plastic hammer or alu block while the three bolts that hold the chuck onto the mouting plate are only lightly nipped on. No mandrel used here but checking with indicator at various stages.
When all was satisfactory I skimmed the base face true. For finishing the bore for honing I utilized an old car brake disc - you find them in all dimensions in scrap containers at garages for free.
The outer face of the disc was skimmed for good finish so I bolted it onto the standard face plate that comes with new lathes . Finally I could machine the bore of the disc for clearance fit of the liner and skim the end face of the disc for zero runout and mount the cylinder onto the brake disc. So in the end that is perfect for boring out the undersize liner plus finishing the spigot of the cylinder liner to get the required preload of 0.02-0.03mm for sealing onto the head - no grinding paste for me.
Another topic: I cannot see why the Vincent engines should really need that much piston clearance of more than 5 thou, that does not correspond to other engines I know. After all, you have an alu cylinder with an iron liner - like modern 2 valve BMWs or Ducati , Guzzi etc. that run happily with ca. 3 thou. So my gut feeling is that possibly the honing operation with the long liner reaching deep into the case is not done with due care. It is extremely important to have all conditions spot on , the correct hone oil, VERY soft grinding stones that don´get blunt and remain free cutting. Otherwise you get all sorts of geometrical defects - and seizures in consequence. I do not use pressure plates and the like, don´t see the use BUT take care to have extra soft stones and lot of oil and keep them free cutting - plus my Zündapp 6 stone production hone.
Just thinking: Could there be some distortion of the liner by torquing down cylinder and head onto the crank case due to funny minmal clearance liner-to-case slide fit?? Positioning the lot via these head studs looks a bit questionable, all drillings not an absolute precision thing it seems.
Vic