Sitting upright is fine at normal speeds but it does restrict your body movement mid corner and also makes it harder to get feedback on what the bike is doing as most of the weight is going through the bottom of your spine which could be why it feels uncomfortable when you up the pace (IMHO!).
If you lean forward over the tank it takes some of the weight off your bum and makes it easier to shift your body around on the bike with your weight now evenly distributed between your arms and legs and you can pick up what the bike is doing more easily and adjust your position/line if necessary.
Try dropping your inside shoulder when you turn into a corner, it'll help relax your upper body and give you a better eye-line through the turn. It might feel strange because your countersteering and putting pressure through the same side but with practice i think it improves your ability to turn the bike.
Regards
Ant