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Okay, so I've been working at a fast food joint for 2 weeks now, and honestly I wouldn't trust ANY of them. Crumbs from everything, get everywhere, things sometimes aren't cleaned just wiped down with sanitizing solution, everyone runs all over the place shouting orders to each other and bumping into each other so it is too hectic to keep track of any one thing.
I would maybe trust Five Guys just because the only things they make are burgers, fries and shakes so you don't have to worry about the fries in the same fry oil as other things etc...
I am in Japan now and staying for 3 months but so far (2 weeks) I haven't gotten sick thankfully. I think basic things to avoid are:
most sauces (they use soy sauce in almost every sauce)
noodles (even buckwheat, unless you can read japanese or know someone who can and they can confirm that it is 100% buckwheat)
On to the positives:
I am lucky, my friend's wife is Japanese so she can check pakaging for me.
A serious investment would be to buy the Triumph Dining Cards.
Japanese are really kind and they understand you have special needs and will help you. I have had several Japanese friends talking to waiters and the waiters were very patient and would go and check on all the food for us.
Tamari (gluten-free) soysauce is available here and I have seen it several times
I have found rice noodles
They have lots of fruit and veggies
Rice crackers (should be checked to make sure they have no flour)
That is all I have discovered so far, I'll try to put more information as I learn more.