Learn English – Explain saw and have seen

All three sentences are colloquially correct when spoken, and totally unambiguous. B would sound more formal because of the words "has been", but otherwise their meanings are all the same.

However, C is the only one which is correct in writing. The phrase "since I have done this…" is (I think) only properly correct when the word "since" is interpreted as "because", as in "Since I've eaten this pie, I'm not hungry any more". It sounds a bit clumsy even in this context.

Personally, in writing, I would prefer to mix B and C:

It has been two weeks since I (last) saw you.

And in speech, I would contract "it has":

It's been two weeks since I (last) saw you.

In speech and informal writing, the word "last" could optionally go at the end instead, but it reads a bit oddly in very formal writing:

It's been two weeks since I saw you last.

When I was in Tokyo, I saw the movie three times.

"was" simple past and "saw" simple past, puts both actions at the same time

When I was in Tokyo, I had seen the movie three times.

"was" simple past and "had seen" past perfect, possibly puts the movies before Tokyo,
to remove ambiguity

By the time I was in Tokyo, I had seen the movie three times.

then there is also

When I had been in Tokyo, I had seen the movie three times.

"had been" past perfect and "had seen" past perfect, possibly puts both actions at the same time