Any food allergy friendly places to eat?

Does anyone know of a list of food allergy friendly places to eat? We will be in Shinjuku (Hilton Hotel), Kyoto (Nakagyo-Ku) and Hiroshima (Komachi Naka-Ku). Would you recommend small vendors as a safe place to eat? Is it common in Ramen places that the utensils used to handle noodles and soup are kept separate from toppings (ie. eggs, pork, vegetables)?

What type of food allergy are you talking about? If it's something like a certain vegetable or fruit, you can often request it not be added, and explain that you have an allergy. If it's more of an allergy to an ingredient, like eggs or wheat, you may have to ask if the dish contains it or if the utensils come in contact with it.

"Is it common in Ramen places that the utensils used to handle noodles and soup are kept separate from toppings (ie. eggs, pork, vegetables)?"

No, they are not kept separately at all. Neither are they at small venders. If your allergy is as severe as that, you should talk to restaurant managers in advance, preferably a few days in advance, or have a reliable conceirge do the talking for you.

Also keep in mind that most ramen noodles contain eggs or egg substances. In other words, if you can eat that, then you should have no problem dealing with venders who use the same knives and tongs for everything.