Narrative tenses

Question

Gary was fed up. He ¹ ______ (wait) for his girlfriend for over an hour and she still ² ______ (not turn up). Just as he ³ ______ (contemplate) going home, she walked round the corner looking please with herself. Her smile ⁴ ______ (vanish), however, when she saw the expression on Gary's face.
— What's wrong? she asked.
— You're late again, he said.
— No, I'm not, she replied, The clocks ⁵ ______ (go back) last night. You ⁶ ______ (be) early!

These are my choices for the narrative tenses:

Gary was fed up. He had been waiting for his girlfriend for over an hour and she still didn't turn up. Just as he had contemplated going home, she walked round the corner looking pleased with herself. Her smile was vanishing, however, when she saw the expression on Gary's face.
— What's wrong? she asked.
— You're late again, he said.
— No, I'm not, she replied, The clocks went back last night. You had been early!

Are my choices good? Are there better options?

Answer 1

Your choices are pretty good, but can be improved:

Gary was fed up. He had been waiting for his girlfriend for over an hour

Good. This one I like.

and she still didn't turn up.

This one I don't like quite as much. The first sentence is in the past tense ("Gary was fed up."), so this shouldn't be in the present for sure. A better option would be "and she still hadn't turned up."

Just as he had contemplated going home,

"Had contemplated" doesn't work here. Her action is interrupting what he was doing, so the preterite is better - "Just as he contemplated going home,".>

she walked round the corner looking pleased with herself. Her smile was vanishing, however, when she saw the expression on Gary's face.

While vanishing is technically a process, it isn't supposed to be one in this case. It is something that happens instantly here. You would typically say, "Her smile vanished, however."

— What's wrong? she asked.
— You're late again, he said.
— No, I'm not, she replied, The clocks went back last night.

Good here.

You had been early!

I'm actually not completely sure here. You have two options. Technically, "You were early" is correct, but I think "You are early" could be used as well, because it is a response to "You're late," and I like the parallelism that that creates. The official answer is likely "You were early," so you should probably stick with that.

Answer 2

Let's take your story change-by-change with some possible fill-ins:

Gary was fed up. He had been waiting for his girlfriend for over an hour and she still hadn't turned up. Just as he contemplated going home, she walked round the corner looking pleased with herself. Her smile vanished, however, when she saw the expression on Gary's face.
— What's wrong? she asked.
— You're late again, he said.
— No, I'm not, she replied, The clocks moved back last night. You were early!

The scenario of the story begins the the past perfect and proceeds to the simple past.

...had not turned up... fits better with ...had been waiting...

Just as he contemplated

moves the time frame to forward to the simple past from when Gary was originally waiting, and fits well with

she walked.

Her smile was vanishing... when

sounds awkward since it leaves the reader hanging, things vanish from somewhere, plausible choices might be

Her smile was vanishing from view... when
Her smile was vanishing from her face... when

However, the simple past

Her smile vanished

is more succinct and has more dramatic effect.

During time changes i.e. standard time, daylight savings time, leap second, it is normal to say that the clocks moved forward or the clocks moved back, the hour change is implied:

The clocks moved back last night.

By this point in the story, the action has moved to the present, Gary was off by an hour, so the simple past simply states this:

You were early.

Answer 3

Past perfect is a complicated tense for even the most experienced writers.

1. Had been waiting is fine.

2. Had not arrived is a better solution, but yours is ok.

3. Contemplated, you are back into "standard" narrative.

"around" the corner

4. Vanished (simple past) is a better solution than continuous past.

5. Turned back last night is a better solution. Correct tense but this is an English idiom. Yours would be understood.

6. Are. Dialogue occurs in present tense unless the character is speaking of the past or future.