@Calum You can have to big a fuelheight, and the engine will be rich. This is possible even without the carb overflooding. if its really excessive, then the bike will spit fuel out the overflow when its on its sidestand. The same goes the other way, it can very well be lean, without running totally out of fuel. When fuellevel is lower than its supposed to, more air can rush by. As I said, af few milimeters makes a lot of difference.
I had this exact problem when i bought mine used. It was only running witch choke on, so the PO assumed it was very lean, and richened it by altering the fuellevel. What was wrong was that all jets were partially blocked, so the bike almost lived entirely of the choke circuit. It didnt run that well 😀
As to the OP, set everything to stock, so you dont have too amny things fooling you. It could very well be a combination of things. Atleast this way you ran rule out a lof of stuff.