"Best way to change currency, find ATM machines? I am a "Credit card"
person, and I know cash is the way to go in Japan."

The best way to change currency is ATMs. Exchanges and banks charge
high commissions. ATMs are all over the place. If you're having
trouble finding an ATM that takes your cards, look for a Citibank ATM.
Credit cards are rarely accepted anywhere in Japan, but it's very safe
so there's no problem carrying a lot of cash.

"Tokyo: I have a half day tour which involves Tokyo Tower, Imperial
Palace Plaza, and the Asakusa Kannon Temple."

The Tokyo Tower is a tourist trap and complete waste of time.

"We will end up in the Nakamise Arcade, and are free for the afternoon.
I am trying to figure out the best way to use the afternoon. I really
want to go to a great shopping district... is this feasible with the
time frame? Is it the Shinjuku or Shibuya region? Will the stores close
soon? What's the best way from Nakamise Aracde to reach this area (also
least expensive)."

Go to Shinjuku. Take the subway to get there - taxis are very
expensive and best avoided except late at night when the subway doesn't
run. If you want to see a Japanese department store, go to Ginza, and
don't miss the food floor.