Since I posted about the warped pump diaphragm housing (bonnet, call it what you wish), I've seen approximately 8 or 9 Carter YF carburetors...various models...and at least 6 had some warpage. In 3 it was enough there's no doubt suction at the bottom of the diaphragm would have brought raw gas in to the manifold. Now every time I go through one, I automatically use the little gizmo I made to see if warpage exists and it is simple to do. Lay the sandpaper on the wood, press the bonnet down and while pressing down rotate for a few turns. Remove it and if you see bright spots where the 4 screws go and dull spots in the center, it is warped. If it is, fix it by rotating more until it looks all nice and even and then stop. Be certain to check the adjustment of the metering rod after doing that. You'll lower the height of the housing a bit and that forms the stopping point for most of the YF models (that and the clip on the diaphragm rod).
Running rich usually just causes the engine to run rough once it warms up and you will smell unburned gas, feel more moisture coming out of your tailpipe and your plugs will be black and sooty looking.
You have a manual choke. I'm assuming you're warming the engine up and opening the choke fully when you set the idle. But let's make certain the fast idle arm is adjusted correctly. On the 2100S, the fast idle arm is designed to rest hard against a stop cast into the throttle body when the choke is fully open. Check to see that when the choke is open fully there is no space at all between that fast idle arm and the stop. If any space is present, bend the rod to adjust and remove it. There is a possibility that if there's some clearance there when you set the idle then once everything gets nice and hot that fast idle arm might move enough to change your idle.
Also your throttle spring...take a look at that. It is a fine balance, I believe. You don't want a spring that's too strong and you don't want one that's too loose. If that spring is too strong I think it is possible when everything gets all warmed up, it could pull hard enough to change your idle a bit...and the trip from 550/600 to 350 won't take much movement. This would tie in with the fast idle arm/stop above. Good luck! Let us know what you find.