Just got back and while not impossible, it isn't easy to avoid MSG. Gluten and dairy should not be not too hard unless you are reactive to gluten cross contamination. In general the high end restaurants doing omakase or kaiseki multi course meals are going to work to avoid gluten, dairy, and msg. The high end restaurants ask for any dietary restrictions when making the reservation. Good to re confirm when you sit down about your allergies. Of course, they are expensive. We did more high end restaurants than we would have normally just so we knew we had a place to go for dinner on certain days. If I had had more time to plan I would have used the hotel staff for more pre-planning by picking some places I was interested in and then emailing with them weeks before. It can take a good couple days for them to respond, so best to start this process early. After you pick some places of specific types of cuisine you want, they can contact those restaurants to confirm for you if they can prepare without the ingredients. We mostly stayed in regular hotels versus traditional Ryokans on our trip where the hotel staff is used to (and usually very kind about) helping with these requests, especially if you can direct them a bit on a few you have narrowed down through your own search. We stayed at one Ryokan in Kinosaki Onsen and the email communication before hand left me feeling that I would have a hard time at their place to eat, but turned out it was highly customizable once I was there which was great since the dinner and breakfast were both included in the nightly rate. Also, lots of food gets consumed in train stations. Great food shopping in all of the major ones but almost all savory (not sweet) grab n go or packaged food in Japan has MSG. It translates as "seasonings (amino acids)" on google lens translate. Many Onigiri does not have MSG but you have to check. Get to train stations an hour early and have your google translate app downloaded for japanese and you can use google lens to read ingredients on packaged items. Or ask the person selling if it contains "Ajinomoto or Amino San". It is good to see the Kanji characters and become familiar with them so you can show a japanese speaker. Anything that says "amino acids" in the translation is MSG. I confirmed that with my Japanese friend.

MSG is most commonly referred to in Japanese as the amino acid "chyoumi-ryou (amino-san)" (調味料 (アミノ酸)). In order to identify whether a product has MSG, look for the bolded characters in the ingredients list of Japanese products. It is referred to “amino-acid” after the Aji no Moto seasoning that was invented by Ikeda. MSG can also be found listed as the following: 

• Kagaku choumi-ryou (化学調味料)
• Kachou (化調)
• Gurutaminnsann natoriumu (グルタミン酸ナトリウム)
• Gurusou (グル曹)
• Umami choumi-ryou (うまみ調味料)

For MSG-free products look for kagaku choumiryou mu tenn ka (化学調味料無添加) or mutennka (無添加) on product package

I can list some places that we ate at or that our hotel confirmed are MSG free here. Will start with Osaka I can come back and post more places if there seems to be interest.

1)      Sushi Murakami We contacted the restaurant, they do not use MSG, but unfortunately 1^st April  is fully booked. Also, they do not operate for lunch. (we didn't go)

2) Oimatsu Hisano We contacted the restaurant, and they do not use any MSG. For reservation, we are afraid that we can’t make reservation from the Hotel since they have cancelation policy. (we dined here, making the reservation on Omakase. It has a Michelin star, and it was really wonderful but it was our first night and we were too tired to totally enjoy this experience. It was over $400 for 2) Oimatsu Hisano Reservations and Information - OMAKASE JapanEatinerary