Unfortunately no bushes in stock, just haven't got round to making another batch. We must sort it out, as some of the others available are quite appalling, with lots of internal burrs from drillings and distortion. Worse still once deburred they are slacker than most worn ones!!
You can run with a couple of thou (0.05mm) or so, overall bush to rocker and pin clearance, never found it an issue. Might be slightly quieter tighter but will probably wear quicker, soon arriving back at the same place! If the spindles are a light tap fit that's good, but it may be a sign of being slightly oversize (not a problem) or not quite true spindles. When the head gets hot the spindles can turn and give you a bigger clearance. May not be the case, but something else to look out for in the future.
Occasionally mysteries like your changing clearances occur in engine building, in my experience it's more often something you haven't thought of or noticed than a mistake. Ducati bevel engines are a minefield of burrs, eccentric components, non square or parallel surfaces, radius's that don't clear there matching components etc etc.... Mostly in a standard engine they don't cause many problems, but they will be behind all those mysterious loose flywheels, clutch centres, crank play etc. The design of these engines is good (exceptional against most competitors of the day), but they were built to a cost by largely unskilled/ semi skilled workers. Working on these engines I generally never take anything for granted and certainly never assume Factory components will be to drawing! I've spent many years honing my paranoia, some of which is probably pointless but the rest has stood me in good stead
Final paranoid thought, as you commented about the seat being proud, are you sure the inlet valve has ample clearance to the piston? (both in depth and radially). A large valve clearance is quite often a sign of a bent valve an a race bike. May also explain mechanical noise, maybe worth looking sooner rather than later! I have been staggered how well an engine will run with a slightly bent valve, so not always obvious. Again may not be the case, but you would be amazed how many engines and components I have seen, where the customer is oblivious to the fact the piston is hitting the head or valves the piston. Alarmingly some of these engines have been "professionally built". When you get into the forensics of engine failure, "this parts crap" is not always the reason for it's failure
Regards Nigel
) the con rod was sleeved as a last resort 6000km ago as it is a 32mm pin set up and rod alternatives were limited at the time.