Check with a doctor, as always, but the toe thing might be an impingment of nerves passing through the ball of your foot into the toes, caused by shoes that are too tight across the widest part of your foot, or pedals that localize the pressure on too small an area under the ball of your foot, or all of the above. Several people said they also suffered with this when I posted about it a while back. Mine has improved somewhat by wearing the thinnest socks I have - no socks might work too if you're into that, loosening up the distal most strap on my shoes to give a little bit more wiggle room in the toe area, and applying metatarsal pads on the liners of my cycling shoes. The pads help to keep the ball of your foot from bunching up, and took no time at all to get used to in the shoe. A podiatrist needs to place them so they are in the right spot, or they might not be effective. I have Look pedals, which provide a fairly large platform, and Sidi road shoes, I forget the model, but they're the black ones. There are not so many shoes available built on a women's last, so I don't have many options there.

Wouldnt venture a guess on the whistling.

Good luck, I hope the pain alleviates soon.

I use specialized body geometry shoes, they have a raised piece on the liner that is supposed to help spread the bones in the foot and prevent numbness. I'm not sure if you can buy just the liners but it may be worth a try.

Have you tried covering gaps and holes on the bike with tape to see if you can find which one is whistling?