A proper analysis of the passage in question is only possible when considering the paragraph that comes before it:
There was no party that night. I had expected one, but the noise never came. I did hear feet walking upstairs around midnight, but that was it. Nothing else. Linc had tried to be casual with his questions, but I could tell he had been curious about Krit. My answers were appeasing him.
When he had walked me to my door, he had kissed me. Like before, it had felt good, and the closeness had been nice. His taste was warm, and the gentle touches of his tongue against mine had been exciting. I had been happy to stand outside and kiss him for hours. But Linc had ended the kiss and then let out a deep breath before kissing me on the forehead and saying goodnight.
This indicates that there are only two mistakes in the passage.
I will edit the passage with brackets to indicate changed verb tenses:
When he had walked me to my door, he had kissed me. Like before, it had felt good, and the closeness had been nice. His taste [had been] warm, and the gentle touches of his tongue against mine had been exciting. I [would have] been happy to stand outside and kiss him for hours. But Linc had ended the kiss and then let out a deep breath before kissing me on the forehead and saying goodnight.
After changing his taste was warm to his taste had been warm, the passage now makes sense—especially in light of the fact that the previous paragraph sets it up to all take place in the perfect past.
Also note that without this correction, the original sentence in question suffers from a lack of parallelism:
His taste was warm, and the gentle touches of his tongue against mine had been exciting.
Without rephrasing it in order to make that mixing of tenses acceptable (something like his taste was warm, just as the gentle touches of his tongue against mine had been exciting), one or the other of those verb tenses should have been changed to match the other one.
As for changing had been happy to stand to would have been happy to stand, it's less problematic but still worth correcting.
Finally, to address why it's not just in the simple past: it can't be because it's an event that's being described as having taken place prior to some of the events described in the previous paragraph—which are themselves described in the simple past.
Note: This is the end of my analysis and you can stop reading here.
What follows is the answer I had originally provided when I had not looked at the paragraph that came before the passage in question.
I provide this only to those who are interested in an illustration of how important context is.
I don't know if I can give a valid interpretation of this passage, because I don't believe the assumption that it's been written as it was intended to be written.
Note that within context, and after making only a couple simpler changes, the issues I'd had with semantics also disappeared.
Let me restate the original passage:
When he had walked me to my door, he had kissed me. Like before, it had felt good, and the closeness had been nice. His taste was warm, and the gentle touches of his tongue against mine had been exciting. I had been happy to stand outside and kiss him for hours. But Linc had ended the kiss and then let out a deep breath before kissing me on the forehead and saying goodnight.
Honestly, I get the impression that this passage is neither well written nor edited. No matter what interpretation I put on the various tenses, I am left feeling confused.
In my mind, I would like to reinterpret the passage so that it becomes something like this (brackets indicate added, changed, or deleted text):
When he had walked me to my door [in the past], he had [always] kissed me. [This time,] like before, it [] felt good, and the closeness [was] nice. His taste was warm, and the gentle touches of his tongue against mine [were] exciting. I [would have] been happy to stand outside and kiss him for hours. But Linc [] ended the kiss and then let out a deep breath before kissing me on the forehead and saying goodnight.
With this revision, I have no problem reading and understanding exactly what's going on; what events are properly in the simple past and what parts are in the perfect past.
There are a couple of pieces I could interpret differently, but the overall edit would be the same: better separation of verb tenses.
I am not at all certain that the book is written in a completely appropriate way. It seems to me that some parts need to be in one tense (whatever that should be) and other parts need to be in a (relatively speaking) prior tense. But it seems that some phrases that should be in one tense have, out of some oversight, been left in the other. This causes confusion because they both appear to be happening "at the same time" rather than one happening before the other and serving as a comparison.
I can't really make a proper judgment, though, because I'd have to see more of the narrative that takes place before this passage.
There is also a semantic (or mini-structural) problem. The passage talks about what used to happen in the past—and then it talks about what happens this time. But there is no explicit difference given between the two. So, the comparison is simply confusing.
I am assuming that in prior experiences they did stand and kiss for a longer period of time, and Linc never stopped like he did this time. It's this fact that makes this particular event pale in comparison and seem strange. Why did Linc stop this time when he didn't before?
No doubt this is explained in the rest of the story. But this contrast between "prior past" and "current past" should have been made more explicit—both in content and verb tenses.
