The way it is written now (the underlined part) is okay, but only okay. If I were to change it, it would be the second sentence, which is currently all in present tense. I would change the second clause to the subjunctive case, which I believe is more grammatically correct than “is here”. This should also take away the weirdness of having the second sentence being completely in the present tense. Therefore, “All that matters is that Miyamura-kun be here”. It is a small change, but it should read more naturally.

The justification for using the subjunctive is a little complex. The clause “All that matters...” is our common colloquial English for what REALLY SHOULD BE “All that would matter is that...”, making it conditional in nature, in which there is doubt as to what truly matters, and even in the most extreme case, what matters in any topic is wholly subjective in nature. That doubt requires the second clause to be expressed in the subjunctive. That is the technical explanation for my suggested change.

In the first sentence, it is right for “will” to be “would” since the nature of the first clause is conditional—“Worst case scenario...”, implying a best case scenario and everything in between. Since there is no total certainty that this will be the actual outcome, namely “you won’t be there”, then “would” is justified. It would only be right to use “will” if there were going to be very high certainty that this will be the outcome, but this cannot ever be guaranteed. That is why “would” is preferable to “will”.

[whew]