I thought it was time to come back with an update.....
After trying the suggestions and finding it didn't make a difference, almost by accident I spotted a completely unexpected problem. The reason it was running poorly and header pipe #2 was cold was because it wasn't connected to the engine ! One of the studs had snapped off halfway down and the header had shifted slightly so there was no backpressure into the cylinder.
I really didn't want to have to take the top end of the engine apart and strip the head in order to remove a thread which has been nicely welding itself in for around 45 years, so I did a bodge. I took a spare collar and filed enough of a slot in it that what remained of the stud would take a nut and washer. Yeah, I know it's not ideal, but it worked !
With all four cylinders working, I was able to get it running reasonably smoothly and synch the carbs successfully.
Sadly, when I came to do the airscrews today, #3 stopped working, and fuel poured out of the overflow pipe. When I drained the float bowl, the fuel included a few tiny black specks, so I'm guessing these jammed the float needle and/or float. So it's time to take the carbs off, clean them yet again and try to work out what's going on.
This has been a constant issue over the last year or two. I've got a fuel filter on (which is pretty new, transparent and looks very clean) so I am starting to think that even with fuel stabiliser the ethanol in modern fuel is breaking down floats, fuel lines and anything else rubber in the carbs. Does anyone have any good solutions to this ? I'm guessing I'll have to replace every single rubber component yet again (mostly they are viton, but I really don't think it makes a difference), and maybe the floats as well.
Are there any bikes with carbs which would swap straight on that are modern enough to be resistant to ethanol ? I'm starting to think that persisting with the original Mikunis is just a road to endless trouble !