Okay. So at the weekend, I took off the tank, airbox etc. I took out the filter and it was dry and clean (the bike was serviced in November). I noticed that the pipe circled wasn't connected to the airbox and it definitely was last time I had the airbox off. Probably those naughty mechanics who serviced the bike didn't plug it on again or it dropped down after not being fastened tight enough. I cleaned and sprayed WD-40 all over the place including into the engine through the air intakes. I also sprayed it over where any pipes went. I checked all the pipes going into the airbox. I left the battery disconnected during the whole time and this may have had an impact too.
I checked the throttle action and it seems fine, but I sprayed more WD40 over both ends anyway. The gold throttle valve thingies shown in the picture were closed and airtight with no throttle anyway as they held a few ml WD-40 fine until I twisted the throttle!
I didn't bother checking the spark plugs yet as the Haynes manual told me I needed to remove and drain the whole cooling system to get to them and I didn't have the time or motivation to do this!!! :spank:
When running, I couldn't feel or hear any obvious exhaust leaks.
When I put the bike back together, it was still running rough and idling high. I used the idle adjust screw and managed to get it down to about 1.1k idle. It was blowing either white smoke or steam out of the exhaust at first, but this went away after running it for 10 mins or so. The next morning the smoke/condensation was back and it was still sounding rough. It actually reminded me a lot of an MT-01 I rode once! The annoying thing is that the bike is fine as soon as I start But as soon as I stop it sounds horrible at idle again. I'll take a video tonight and upload. I may have to take it to a garage as I've done no engine work at all before and don't want to make anything worse!
So in summary: it's better than before, but there is still something wrong!