Are there any hills on your route? What difference is there between the performance riding uphill and downhill? Rich condition performs better going uphill, and it "four strokes" going downhill.
Is there any throttle delay? Presumably not since we're pretty sure it's running rich.
Stalling any time you use even a little choke means that it's very rich.
Choke restricts the airflow without affecting the fuel flow, so that it richens the a/f mixture.
On a"perfectly" set up carb, in the cold weather it's normal to need some choke until the engine warms up, so I'm pretty certain it's already rich.
Rich is good for break-in stage but it could be just a bit too much of a good thing.
It might need a smaller jet. This is something that I have been able to avoid until the engine is broken in. What I mean is that with your engine being in the break-in stage, and with the cold weather too, it's a bit strange that you should need a leaner a/f mix already.
So perhaps you should check for leaks around the head gasket.
Also maybe test the compression. A stock engine fitted to the bike without any modifications may well have a low cranking pressure. Raising compression (within safe limits) will give you a bunch of extra torque. So you might want to buy or borrow a compression tester and find out what the cranking pressure is on your engine.
I'll probably pick up a compression tester tonight then and hive that a go. I always appreciate the help thanks. I will post what the test is.