A few years ago it took me a while to work out that my bad idling 851 was due to a combination of the soft closing springs the early 851 ran and large closing clearances. I had adjusted the clearances before I got it back on the road after the post sale cosmetic strip and reassemble, but I'd also fitted new steel collets in place of the original stainless ones they ran on 88 and 89 models and the clearances had settled a bit, no doubt helped by the 104 dyno runs it's had. So by the time I parked it last it'd done 6,000km or so since and the idle had deteriorated quite a lot.
The soft closing springs contribute, and I've had to work on a couple of bikes over the years that just wouldn't idle due to the soft closing springs some people fit in belief they'll make more power. Basically it's over 2,000 rpm ok, under 2,000 rpm stall.
The ST3 and 996 issues associated with the closing springs and clearances reiterate how important it can be to general running at lower speeds, and I recall one early 851 owner (possibly of the bike I own) saying it ran so much better after a big service.
Anyway, I got bitten by the excessive closing clearance thing a while ago on a MHR Mille bevel drive. It arrived after having a big service, etc, by someone else and "just needed a tune" to finish it off. So I tried to make it idle. After 15 or so hours of replacing lots of worn out carb bits and checking every thing that I could think of, it still wouldn't idle. I mentioned to the owner that I'd run out of ideas, but maybe it was valve clearance related even though they'd "just been done".
So the owner gave me the go ahead to check the valve clearances. Turned out there was around 0.15 - 0.25mm play in the closers, with the openers largly ok. I took the closers down to as close to 0 as possible, put it back together and hit the button. It idled long enough dead cold to let me know it was better.
More recently I had an ST2 in that had 140,000km on the clock and had just had the heads off. Nominally it'd come in for throttle body set up and eprom to suit the Staintunes, but once I'd done the TPS baseline and fired it up I knew something else was wrong. Namely, it wouldn't idle. Which was one of the things the owner had mentioned. Again, the valve clearances had just been done, but it was the most obvious thing for me to check. And again there was around 0.15 - 0.25mm play in the closers, with the openers largly ok. I took the closers down to as close to 0 as possible (much easier on a belt drive than a bevel), put it back together and hit the button. It idled dead cold like most of the injected bikes will and I finished the tune from there. The hydrocarbon emissions were a little on the high side possibly indicating some valve guide wear (they hadn't been done), but apart from that it was fine. And ran much better.
I have had 1000DS motors in for valve clearances where i've added 0.15mm to the closing shims to close the clearance up too, although most are in the 0.05 - 0.10mm range. I sometimes question whether it's worthwhile adjusting a 0.05mm clearance on a 2V bike, but it appears it is. I do find though that many of the 1000DS cams have a tight spot at the end of the closing lobes just as the valve starts to open. You can feel movement in the valve when rotating the cam around the base circle, but it will rub as you get to the lift points at either side. So there's always going to be 0.02 - 0.03mm clearance at TDC firing to allow for that.
On the 4V bikes I always take the exhaust closing clearances down to 0.05 - 0.07mm and the inlets to 0.08 - 0.10mm, going to the tight side if the collets are broken and have to be replaced. I've not owned a later 4V bike to know if it really makes a difference you can feel, but it doesn't hurt.