The latest.
The mechanic phoned me the day before I was due to pick up the bike as he wanted to go through what he had done before I arrived as he was not working on the Saturday.
So jobs done:
1. Checked and reset mixture parameters
2. Injection system checked for fault codes, non apparent.
3. TPS was set at top limit, reset to middle (apparently it is numbered 15,16,17)
4. Idle speed reset (raised a little)
5. Compression checked.
6. Plugs checked.
7. All engine sensors checked.
8. Checked fuel pressure to injectors 3.5 bar, 49psi.
9. Voltage check to injectors.
10. Co settings changed, In Italy I noted 5-,8,8,11 and they now read 8,8,8,8.
All the above with Yamaha picking up the tab.
I started the bike up on collection and it seemed okay. Starting it yesterday gave a little sign of the tick over miss but it was a lot better and I can live with it (only does it on first start-up of the day). The other difference is that the slight hesitation from closed throttle to open has gone, the bike is a lot smoother and seems more much more powerful in fact a lot more powerful. The vibration at over 80mph is still there but that may go in time as the miles increase. The bike also seems to use less fuel as I've now done two rides and I'm getting 130 miles to half a tank so maybe an extra bonus. As for the power loss this is still being investigated. As I don't have any high roads near me I can't test for the altitude issues.