I've been struggling to figure out what kind of code or chemistry could accompany a post like this. But I think I'll just play it straight and share some recommendations for things to eat in Japan.
Specifically, the Bokkake Soba that is sold at 神戸灘八 here in Kobe. My understanding is that in the Nagata ward of Kobe, there is a famous local food called "sujikon", which is a mixture of beef tendon and "konnyaku". At 神戸灘八, they make a kind of noodle dish, which comes with sujikon, egg yolk, etc. It has a similar profile to ramen, but it really has a unique flavor.
Sushi restaurants often serve a red miso soup which has fish trimmings in it. It's really good, the soup has a deep and heavy flavor. If you're like me, you might walk away from a restarant thinking that was the best part of the meal.
Apparantely I really like noodle dishes from Hyogo prefecture. In this case, the choice of meat is "Horumon", which I think translates as "offal" (i.e. various organ parts from the animal, specially cows in this region). The sauce is more on the sweet side. The main place to get it is the town of Sayo, which is about an hour from Kobe by train.
Oyaki is another difficult one to find, being limited to the Nagano region. It is a kind of dumpling made from buckwheat, and it comes with a variety of fillings ranging form sweet to savory. If you like chinese style dumpings, I think you will love Oyaki.
This one feels silly, but I promise you will enjoy it. Many of the fast food restaurants here serve an affordable, rice-based breakfast. Nakau distinguishes itself by having the best over easy eggs (目玉焼き) and bacon. Granted, it's not American style bacon, and in my experience I can make a better version at home, but at least go and get a sense of it. Nakau also has the best miso soup of the chain restaurants.
Honorable Mention: Shio Saba
I'm surprised I had to leave this as an honorable mention, as it was really the first thing I loved after arriving. In my childhood experience, fish was always served without any skin. This style, by contrast, has the skin on, which leads to a very fatty taste. When combined with a lot of salt and lemon, it's great.