Try the tomato juice on a small hidden area first, like the bottom of the bottom bracket.
I had a Chessie retriever years ago that would catch the occasional skunk and get sprayed, and for him I used a diluted white vinegar and water mix that worked fairly well. Just had to keep it out of his eyes. Killed the skunk smell pretty good, not as messy as the tomato juice, and just made him smell like a salad for awhile, and a salad smells way better than a skunk. But, again, test it on a small hidden area on your bike first. Not sure if it will work on the shoes.
The other option is to just let everything sit out in the sun, then hope you never get caught in the rain.