When I worked in Tokyo 8 years ago, my boss took me out to an expensive sushi joint at the top of a Shinjuku hotel. (Hilton?) He expensed it, told me it was a few hundred dollars, and told the chef specifically what to make- no menus in sight. The sushi melted in my mouth, and I tasted roe I've never seen since. Also had some pygmy melons that seemed pretty tasteless, given their delicacy.

I would say this- if you are going to spend the money, make sure it is really a special, reputable place, and not just expensive for the sake of being expensive. I could certainly taste the difference, but I don't know if I would spend that much for a meal under too many circumstances.

Not if you are looking for cherries.

or miracle fruit-su.

Your first point is very true even in areas in the US with a sizeable Japanese and other Asian population like San Francisco and San Jose. The great sushi places in the SF area are small, hidden places and very expensive. In Tokyo, even the sushi-boat places (kaiten zushi) have generally good quality seafood at a value price.

Your second point is true and but it may be a little difficult to detect the chef's reluctance to serve certain items unless one is accustomed to Japanese (or various Asian countries') politeness. If one detects a slight hesitation or grimace, or even an inspecting glance at the inventory when one asks for a certain item, it might be that the chef doesn't really want to serve that item, and one would be advised to wave the request away and ask for something else or let the chef decide.

To the OP's question about tuna. Maybe you heard about the fresh, raw tuna used for sushi and sashimi and not canned tuna? You don't need to spend $200 for awesome sushi in Tokyo. You do however might have to wait in line. The good (to great) places have very reasonable prices (Y3500-4000 for a deluxe set) and the lines will be long. Off the top of my head, I'm thinking of places like Sushi Dai, Daiwa, or Bun in Tsukiji.

Shrines
 

I'm not at all an expert on Shinto shrines, but here are a few of the ones I thought were worth seeing (I also recommend the Miyajima shrine mentioned earlier):

Fushimi Inari Taisha in Kyoto - has a path that is lined with hundreds (thousands) of torii, like going through a tunnel of torii. Makes for good photos.

Toshogu in Nikko - Tokugawa Ieyasu is buried here. My understanding is that this is not a very traditional Japanese shrine, it has heavy Chinese influences. It's incredibly gaudy compared to most shrines, with gold leaf, detailed engraving, and vibrant colors everywhere.

I'm not sure if you have a specific interest in Shinto shrines, but the other major religion in Japan is Buddhism, and there are also many Buddhist temples that are interesting to see - off the top of my head I would say Kinkakuji and Kiyomizudera in Kyoto and Todaiji in Nara.