Very intersting read as always Nigel and a very good point made re:tolerances.
I have been reading this thread with added interest as I have been re-commissioning the 400/4 I originally restored 28 years ago over the past month or so.
I havent used the bike for 13 years as its been laid up due to other bikes/work/DIY etc getting in the way. It was always a case of 'I'll get that running in the spring' only for it never to happen! The bike has only covered 7.5k miles between 1992 and 2006 after the engine was fully rebuilt. Oli changes were completed every 1000 miles and its always been kept in my garage. I drained the old oil a couple of weeks ago and it looked like ATF, I remember when I bought it at the time and it was that colour, I have no idea of the brand but it was the correct motorcycle oil and bought from my local bike shop. The condition of the oil was as-new and so was the filter but I am changing them anyway as the oil is too old to leave in there.
Having read the start of this thread I bought some flushing oil but to be honest, after reading your reply and the potential damage (IMHO) of what flushing oil could do Im not going to use it. Instead I'll buy some cheap oil (to the correct spec) and run the engine for 200 miles, drain it and change the filter.
I've had the rocker cover off, all the valves are moving and I have no rust in the bores (using my endescope). I'm going to drop the sump and take a look at its contents and check the tensioner horseshoe is ok. I know there has been discussion about sticking rings/ gummed-up rings etc but this is a chance I'll take.