Thanks Tomatocity, I did check the the vacuum caps were seated, but didn't pull them to check for cracks... however... funny story...
I'm staying with a great Turkish guy in Ankara (actually all the Turks I've met have been very friendly and enthusiastic about helping me), and so of course when I had a day pulling the bike apart, he wanted to help (he has a GS1200). I said really, it's OK, it's only a one-man job. He said he understands, but then would be sticking his hands in everywhere - whenever he saw what I was trying to do, he would be in there doing it. Now, I hate having someone even looking over my shoulder as I work, let alone someone helping me who doesn't know what he was doing. He was also pretty gung-ho about it, whereas I'm more slow and methodical. I tried to get the message across that I really didn't need any help. He speaks some english, but language was a bit of an issue too. I really didn't want to offend him, he's been a great host... So I just tried to keep an eye on what he was doing, stepping in when I wasn't happy.
But what always happens when I'm working on a bike and get distracted, is that I forget something. In this case when reassembling the airbox, I forgot to tighten the clamp on the right-hand throttle body. This is the real reason I don't like anyone helping me - not only do I have to watch for their mistakes, I end up making them myself.
I took the bike for a ride and it was a bit better, but still surging at small throttle openings. So decided we had to take it to a mechanic that was highly recommended. (I thought step 1, do a throttle body sync, he would have the equipment) Three of us ride across Ankara (GS and another S10) to a grubby little workshop. Mechanic takes the bike for a ride around the car park, comes back with his diagnosis. TBS, yes, but also it's overheating (yes you just rode it around the car park and the fan came on), it has low compression (?) and needs a new clutch (WTF). All from 2 minutes around the car park.
I said OK, lets do a TBS first. OK leave the bike, it has to be cold to do that. No it doesn't! Eventually I lift the tank to do the TBS and he has no clue where to start. We need to find a turkish service manual. While the tank is up I check the clamps and find the loose one... I say ok lets forget about this until we get the service manual, I put the bike back together and test ride - huge improvement now it's not sucking air where it's not supposed to be. I try to explain what's happened but they are still worried about low compression and bad clutch. The mechanic wants me to leave the bike so he can check valves when it's cold. No chance mate! Anyway it had a valve check only 13000 miles ago, so that is not going to be the problem. The clutch feels fine to me, so I took the other S10 for a ride, it is at 40,000 miles and had a new clutch basket 10,000 miles ago. I couldn't tell the difference between his clutch and mine... So in the end I said thanks, but I don't need you to do anything.
So maybe it does still need a TBS but that's not the cause of my issues. I had found water in the No. 1 plug cavity, maybe that was it? But replaced all plugs anyway, at 12,000 miles it's well before I would normally change, but right at the recommended service interval.
Seems to be running pretty well now, I've ordered the O2 eliminators and a fuel filter sock (I haven't looked at the filter yet, but that will be next) to be delivered to Georgia, so should have them in a couple of weeks.
On another subject, I got my Iran visa yesterday! So looking forward to meeting some Iranians...