Sometimes people are upset at no on in particular, they just need to work it out on their own. This is one of those things.
You shouldn't reach out to the student unless you really know what you're doing. The student might not be happy about you reaching out and complain to the university. You have no duty to reach out either.
Sometimes instructors offer additional work (such as an extra project or assignment) for credit to let failing students bring up their grade. If you have an actual deal of this sort you can offer, that's a fair reason to reach out. But if the student already got a D, it would be hard for you to move the grade by more than a letter without it being unfair to other students - especially if they didn't know that such an opportunity would be offered! So even if you go above and beyond for this student, their grade would at best be a C, which isn't much better. They're better off just retaking the course. If they retake it with you, it might be a pretty good idea to start a dialog (privately) about what parts they struggle with the most. You can frame it as wanting to improve the course so the student doesn't feel singled out for failing.
Don't worry too much about the time - it is what it is. Some people give extra time at the end of exam - but if you've taken 2 hours to do an exam other people did in 1.5, you've probably had all your best ideas already. Even an additional hour is unlikely to make a difference, unless the exam was specifically designed to gauge speed of work (if it was, you wouldn't have so much variance in how quickly they finish). If the student complains, you can point out that everyone gets the same amount of time, so giving an extra ten minutes is already special treatment for that student at the expense of everyone else who didn't get extra time. You would already take the overall class performance into account when grading, so if everybody had done poorly in that timeframe, presumably the best students could get an A despite not getting every question right.
Also, the final is a bit late for interventions. There's not much graded material left... Unless the student does retake your course, or comes to you for help, there's nothing you can do here - the ship has sailed. For future students, you can play close attention to early midterms and quizzes, and act accordingly during office hours, lectures or when providing study materials. Inevitably, some people in every class will score low. If you really want to prevent this, you can build in "second chance" type rules in your syllabus: For example, option to do a project for extra credit, or dropping the lowest mid-term mark from the average. If you put these in the syllabus and make them clear in the beginning of the course, it's a lot easier to help failing students overcome their low exam score while still being fair.