Series 60's don't wear much but the main problem is liner protrusion height. From a negative .0005 to positive .003 is allowed. When building one the liners need to be a
minimum of .002 above the deck surface on a DDEC 3 12.7L or DDEC 4 14.0 L. The completed one is a 14.0 L the one in the frame is 12.7 and only a head gasket was
being replaced. The complete rebuild had 525,000 on it at the time it went on it's side over wound and bent the valves.
I would correct your cylinder problems throw the head back on and run it. No point in messing with the gear train in the front section if the gears look ok from the bottom, IMO.