That's a lot of questions for one post.

First of all, the stops are so close to each other only if you're looking at a schematic map. The Tokyo-Yokohama subway system covers a much greater surface area than either the London or Paris systems.

If you have time, I suggest buying either the Kodansha Tokyo City Atlas (not updated since 2004, but the basic landmarks are mostly the same) or the more up-to-date and pocket-sized Bilingual Atlas of Tokyo, which appears to be available only in Japan.

You may have heard of Tokyo's decidedly non-Western addressing system, based on a series of progressively smaller named and numbered units: wards (ku), neighborhoods (cho), areas (chome), blocks.

Both these atlases manage to cram bilingual versions of all these designations plus the names of major buildings into a series of area maps, so if you want to wander around the Ginza, there are close-up maps of it in both books. They clearly show the subway and surface train stations, and the Kodansha atlas even shows which numbered exit to go out of to reach your destination, although there are also bilingual signs inside the stations that give these directions.

Once you are in a subway station in central Tokyo, there is a map on the wall that shows only the central subway lines, with color-coded lines and numbered stations giving the fare to each destination. I've taken a number of first-time visitors on their first subway ride with transfers, and they have been surprised how easy it really is.

I'm not sure, but I think that if you are coming to Tokyo from elsewhere, you can't buy a Suica/N'EX ticket. Since I haven't taken the N'EX to Narita for a few years (I usually take the Keisei Skyliner), only from Narita, others may be more up-to-date. However, in the grand scheme of things, a N'EX ticket isn't all that expensive, and you can buy a Suica at any JR Station (or its sister card, PASMO at any subway or private rail station) from bilingual vending machines.