Usually restaurant sells lunch set menu around lunch time for ¥1000. They don't sell lunch set menu in dinner time. Alcohol drinks around ¥600 in the evening.
Eating in Japan you need to use a website called Tabelog. It's useful to check the score of a place (3.5+) and their business hours.
Tabelog did not simply count the score by average of everyone, they have a formula1 that a shop needs to keep getting reviews to increase the score (A newly opened place, even though it's a good place, you may see 3.0-3.2, it's still ramping up.). A Power User (who have a lot of reviews on Tabelog)'s high review weights more. The score updates every first and 3rd Tuesday of the month.
In General, 3.5 on Tabelog is popular, usually satisified customers. If you search on Apple Maps, it shows you Tabelog score in the search result. Popular and satisified do not mean delicious in my opinion.
In the city, a lot of places have 3.5+ scores usually because of cheaper price, the location is good (Especially Ramen).
A lot of people may hit the ceil of 3.8, because recent scandal reveals 2, if the shop does not pay Tabelog, they will not get over 3.8. They will stick around 3.6.
All in all, 3.5 is still a fine bar. But they're a lot more things to dig in from the reviews.
Recommendations from good friends are still the trustworthy index.
If you can't use Tabelog
Get in the line. Japanese people are the most patient people who are willing to do the research for food and wait in line, so trust them! But avoid lines look like all tourists and in the weekend.
Before you go
Check the shop's twitter / SNS, restaurants in Japan operates in complex hours, every shop sets their own business hours (because they can!). They usually have a last order time so you need to get in before that. They have breaks in between lunch and dinner time. Check their official off dates and opening time. Usually they will announce a sudden off time. Best ones usually off irregularly, only do lunch time, or if they still have ingredients.