So, a couple things about foot position from someone who recently crushed his ankle...don't settle on just one.
As mentioned, I crushed an ankle. My doctor was expecting to remove my foot, but it somehow survived. Since recovering, what I have discovered for confort and handling is that you really need to position levers exactly where your relaxed appendage will just contact them when you put aforementioned appendage in place. Otherwise, get that foot out of there if it isn't shifting or braking at that exact instant. Your foot should be positioned with the ball of your foot on the peg...NOT your heel. This keeps your foot from being captured and broken during turns and also allows easy weight transfer for handling. Additionally, it allows you to flex your ankles while riding so that your muscles don't get stiff.
Another thing to keep in mind is that your shifting shoe should provide instant contact with the shift lever for both down and upshifts. If you are flexing your foot a lot to reach the shifter, then you are unnecessarily straining your ankle muscles. Sneakers would create a situation like this.
Experiment to find what is most comfortable...and keep your HEELS OFF the pegs unless you are actively shifting or braking.
Regarding stiff wrists, you should not have any weight on your hands while riding. Resting on your hands screws up your handling abilities and is the primary reason for endoing when losing traction during heavy front braking (the wheel won't turn if you aren't leaning on handlebars). Instead, you should hold the motorcycle with your legs (the real reason for grippy tank pads - contact points for your knees) and maintain your posture with your stomach and back.
Knowing how to sit on the bike is just as important as knowing how to ride it.
Regards,
Camelman