Determining sequence

I have a question regarding determining the sequence of events.

"It is taking her a bit longer than usual to get back on the game because she had come back from Germany last night. So I gave her a friendly warning just now and she promised me that she would try her best to pull herself together.

1. "It is taking her a bit longer than usual..."—happening now, so I used present tense

2. "had come back from Germany last night"—about last night, so I used past perfect

3. "I gave her a friendly warning just now"—about what happened a bit before now, so I used simple past.

Is this logic correct? According to what I've learned so far, I think I must use "had come back", since I was talking about what is now ("it is taking her a bit longer than usual...") before talking about her come back from Germany, and I talked about what happened about 10 minutes ago after talking about last night. But then, I do think that I'm kind of reporting events in chronological order and "had come back" just sounds so weird to me.

Another question--

"Big brother thought you bought too many flowers, so he looked at Mom's text message that asked you to get some flowers. Since he couldn't really figure out what 'some' meant, he decided to call Mom. He has just confirmed with Mom that she never asked you to buy so many flowers. Since what you bought is way more than what she needs, I will return them. She might ask you to go buy some more if she runs out, though, so I don't see why he is going to return them."

I saw the example above in a friend's email (I tweaked it a little for practice). I can't figure out if the tenses are alright. It seems like they are all over the place. My main question on this one is: Can you start off with past tense to talk about a past event and then use present perfect for a slightly more recent event?

• Personally, I think the past perfect "because she had come back" is actually wrong, because it clashes with the earlier "It is taking...". In any case, it contributes nothing useful to the sense - so at best it's stylistically clunky, to my mind. May 5 '13 at 20:17

My main question on this one is: Can you start off with past tense to talk about a past event and then use present perfect for a slightly more recent event?

The present perfect tense is used (among other cases) for something that is relevant later. You could use the present perfect for a more recent event, or for an event happened earlier than another one.

She has arrived home. She called for pizza delivery twelve minutes ago.

"She has arrived home." means she is still at home, while "She arrived home." doesn't say anything about where the person is at the moment, although that could be clear from the context.

She arrived home. She took a shower, and she called for pizza delivery twelve minutes ago.

If you want to make evident that an action has been done before another one, you would probably use the past perfect tense, like in the following sentence.