It turns out that the runes in this segment actually represent romaji (transliterated Japanese), rather than German (which is more commonly the language represented by the runes). Jon Lin's comment links to a Japanese blogpost that has done the gruntwork of converting from runes to Japanese.3 I trust they're right; I only double-checked the first few lines of the runes myself.
The structure of the text here is as follows: everything that isn't in white runes is a line said by someone other than Homura at some point in the series. Pink is Madoka; yellow is Mami; blue is Sayaka; red is Kyouko. The text in white, however, is original (i.e. not spoken at any earlier [or later] point in the series), and is "spoken" by Homura (addressed to post-wish Madoka). There does not appear to be any relationship between the positions of the Homura and non-Homura lines.
Here are the non-Homura lines in order from top to bottom and left to right (translations taken from the official subs on the movie BDs), with annotations indicating where in the series they're from.
Madoka: I'm the Nurse's Aide in our class.
[ep 10, timeline 1 / 32:37 in movie 2]1
Madoka: Homura... I'm really glad I became friends with you.
[ep 10, timeline 1 / 37:45 in movie 2]
Mami: I'm not afraid of anything anymore.
[ep 3 / 45:17 in movie 1; ep title quote]
Sayaka: Give that back! That― That belongs to Mami...!
[ep 3 / 48:24 in movie 1]
Kyouko: How do you even call yourself human?!
[ep 9 / 8:13 in movie 2]
Madoka: Even now, the fact that we were in time to save you from that witch... It's one of my proudest accomplishments.
[ep 10, timeline 1 / 37:51 in movie 2]
Kyouko: Want some?
[various; ep 6 / 81:54 in movie 1]
Madoka: Don't talk about Mami that way!
Madoka: You too― I swear I'll never forget you either! I'll never forget... the way you saved us yesterday!
[ep 4 / 56:00 in movie 1]
Mami: You don't read between the lines very well, do you? I'm telling you I'll overlook what you did this time.
[ep 1 / 18:01 in movie 1]
Madoka: ...why are you always so cold?
[ep 7 / 94:10 in movie 1]
Mami: Will you really stand and fight with me from now on? Will you really stay with me?
[ep 3 / 43:05 in movie 1]
Sayaka: There's no way I'll ever regret it.
[ep 5 / 69:40 in movie 1; ep title quote]
Sayaka: Miracles... and magic... are real!
[ep 4 / 58:30 in movie 1; ep title quote]
Kyouko: I know you don't want to be alone.
[ep 9 / 26:18 in movie 2]
Kyouko: ...on the one thing that means most to you...
[ep 9 / 25:40 in movie 2]
Madoka: So, is it okay if I call you Homura, too?
[ep 10, timeline 1 / 33:19 in movie 2]
Madoka: You... finally called me... by my first name... I'm... happy...
[ep 10, timeline 3 / 49:01 in movie 2]
And here are the Homura lines, roughly translated by me. It's kind of lyrical/songy, and I don't really get what some of the lines mean (like the one about "a day of blue" [うつろいゆくこの全ては青の日の希望の比喩に過ぎません, guessing at the kanji]), so this is not a good translation. I welcome improvements.
Even if I can't hear what you say,
your words touch me deep within.
You take on the forms of all sorts of things
and shower sparkling dust.
Whether above the city or beneath the waves,
you are my only friend.
Though you never call for me,
you are always there.
All these impermanent things are
but a metaphor for hope on a day of blue.
All that came before
is now fulfilled.
Even the magic I could not put into words
can reach this place.
One day, your eternal wish
will come to take us away.
1 There's a slight oddity in this line - in the movie, Madoka says 「私、保健係なんだ」 while in the runes, she says 「わたし ほけんいいん なんだ」. They mean pretty much the same thing, though.
2 The scene where this line is said (Homura and Madoka at the restaurant, with Homura telling Madoka to give up on Sayaka) is omitted from the movie, but would start near 71:06 had it been present. This translation is taken from the Crunchyroll subtitles at 11:50 of episode 5.
3 Twitter user @Fau3 did a very nice re-rendering of the credits with the runes replaced with their corresponding kana (lower-res stack.imgur mirror), which may be of interest to readers.