This sounds like a vacuum leak to me. At cold start, the secondary throttles move wide open, and the mixture is rich. As the bike comes up in temp, the fast idle circuit stops, and it slowly begins leaning out the mixture. So the reason it may be working well at cold start is because the mixture needs to be rich anyway, and once the engine starts to warm, it is staying way too rich.
I know this from experience too, because the first time I was learning to do the throttle valve sync, you have to remove the vacuum lines, and I forgot to unplug the vacuum pressure sensor. So the bike ran so rich it filled my street with smoke and smelled like strong exhaust fumes, and it wouldn't idle unless I raised the heck out of the idle RPM adjuster.
If you have a vacuum leak where the lines run on the throttle bodies, it will force your bike to run super rich, and fail to idle, like mine did. There won't be an FI light for the vacuum leak I don't think, but you can test for the leak easily. You can easily verify or rule out this issue by trying some of these things:
- unplug the vacuum pressure sensor, and try running the bike. By doing this, you force the ECU to guess at a normal vacuum pressure, and the FI light will come on. Don't worry, nothing is wrong, but if you do this and the bike suddenly runs normal again, you almost certainly have a vacuum leak, or less likely, a faulty vacuum pressure sensor. This is usually on or around the airbox.
- Check and clean the vacuum hoses. Sometimes they wear through when the rubber gets old and hard, or they get kinked, or they fall off the throttle bodies. I would suggest removing the vacuum hoses, clean them off in a sink with water, and verify there is no cracks in them or broken T fittings, and that the sensor input where the hose connects isn't clogged or damaged. It has to have an air-tight seal to work. But again, do the first thing I mentioned first, it's easier, and this is more of the fix or subsequent test.
Refer to the shop manual, be careful with the small bits in there, parts can be fragile and sensitive. Don't use pliers to pull the vacuum lines off the throttles, you can damage the hoses.
Hope this helps. A free test to see if this is your problem is worth your time.
-Mike