The Chafetz Chaim in his preface seems to address all your questions (and then some!). While the entire preface (and book) is well written (not that it needs my approbation!), I will try to quote some of the relevant bits that more directly address your questions.
Does anyone know of good sources for Hilchos Lashon Hora from before the Chofetz Chaim?
Other than a chapter in the Mishnah Torah and a section in Sha'arei Teshuva, it seems like there was never an organized collection of Halachos dealing with Hilchos Lashon Hara. There were earlier authorities (the Chafetz Chaim also mentions the Smag and Teshuvos Maharik) that mentioned Lashon Hara related Halachos, but they were never organized in an easy to find manner.
וְכָל אֵלּוּ הַסִבּוֹת עִקָּרָם הוּא מִצַּד שֶׁלֹּא נִתְקַבֵּץ בְּמָקוֹם אֶחָד עִנְיַן לָשׁוֹן הָרָע וּרְכִילוּת, שֶׁיִּתְבָּאֵר בּוֹ אֵיכוּתָם וְעִנְיָנָם בִּכְלָלֵיהֶם וּפְרָטֵיהֶם, אֲבָל הֵם מְפֻזָּרִים בַּשַּׁ"ס וְרִאשׁוֹנִים. וַאֲפִלּוּ הָרַמְבַּ"ם בְּפֶרֶק ז' מֵהִלְכוֹת דֵּעוֹת וְרַבֵּנוּ יוֹנָה בְּשַׁעֲרֵי תְּשׁוּבָה, שֶׁהֵם עָשׂוּ לָנוּ דֶּרֶךְ סְלוּלָה בַּהֲלָכָה זוֹ אַף עַל פִּי כֵן קִצְּרוּ מְאֹד, כְּדַרְכָּן שֶׁל רִאשׁוֹנִים
And all this proceeds — for the most part — from the laws of lashon hara and rechiluth not having been gathered into one spot, where there could be elucidated their nature and application, in principle and in practice. Instead, they are scattered in the Talmud and in the Rishonim (the early authorities). And even the Rambam in the seventh chapter of Hilchoth Deoth and Rabbeinu Yonah in the Sha'arei Teshuvah, who have paved the way for us in this area, have, nonetheless, been very terse, as is the way of the Rishonim.
What are the sources for the Sefer Chofetz Chaim?
The Chafetz Chaim writes that he added footnotes for every Halacha he wrote, and he called that section the Be'er Mayim Chaim. While I have seen a printed version of the book that does not include that part, almost all versions I've seen have it printed on the page (either below the main text, or surrounding it. Sefaria has it under the 'Commentary' tab in their sidebar).
וּבֵאוּר סָבִיב לוֹ יִקָּרֵא בְּשֵׁם בְּאֵר מַיִם חַיִּים, כִּי הוּא הַבְּאֵר שֶׁדָּלִיתִי מִמֶּנּוּ אֶת מְקוֹר הַחַיִּים הַפְּנִימִי.
[My translation] And the explanation surrounding [the main text] is called the Be'er Mayim Chayim, since it is the 'well' from from which I drew the sources for the main text.
Did the Chofetz Chaim innovate!?
He says he did not.
וְיֵדַע אָחִי הַקּוֹרֵא, שֶׁאֲפִלּוּ כָּל דָּבָר פָּשׁוּט שֶׁנִּמְצָא
בִּפְנִים, הֶרְאֵיתִי אֶת מְקוֹרוֹ בִּבְאֵר מַיִם חַיִּים. לְמַעַן
יְבֹרַר לְעֵינֵי הַכֹּל, שֶׁסֵפֶר זֶה לֹא חִבַּרְתִּי עַל פִּי מִדַּת
חֲסִידוּת, רַק עַל צַּד הַדִּין.
And let the reader, my brother, know that for even the simplest thing
found therein, I have indicated its source in the Be'er Mayim Chayim,
so that it be clear before the eyes of all that I have not written
this book according to the parameters of chasiduth [saintliness], but
according to the parameters of din [Law].
The Rabeinu Yonah is somewhat of a bridge between the Mussar side and Halacha but he is primarily a mussar sefer ( the CC admits this).
The Chafetz Chaim does address this, as you mention, but he doesn't conclude the same way you do. He writes that some may ask why he relies so heavily on Sha'arei Teshuvah which many consider a 'Mussar' sefer instead of a 'Halachah' sefer, but he disagrees with the premise of the question and says that the Sha'arei Teshuva is written in quite an exacting language and does not go beyond the parameters of Halacha.
The Chafetz Chaim does concede that the Sha'arei Teshuva does not write the sources in his book (which is not unusual for works of that era), but he writes that all the sources are based on the Gemara, and in addition to that, when the Chafetz Chaim quotes the Sha'arei Teshuva as a source, he will usually bring an additional source for the law, to not solely rely on what some would call an unsourced Mussar sefer.
למה אני מביא בכמה מקומות ראיות מספר שערי תשובה לרבנו יונה, שהוא מכלל ספרי מוסר, כי באמת נראה לעינים להמתבונן היטב במאמריו הקדושים בכמה מקומות, ששמר ודקדק את דבריו שלא יצא מגדר הדין, ובפרט בדיני לשון הרע שלו, בכל ענין וענין שכתב יש על זה מקור מן הש"ס, וכאשר נבאר, אם ירצה השם, בפנים הספר
[My translation] Why am I bringing proofs in many places from the book Sha'arei Teshuva from Rabeinu Yonah, which is a work of Mussar? In truth, if one would delve into his holy words, you would se that he was careful to be exact in his wording to not go beyond the parameters of the law, and in particular in the section on the laws of Lashon Hara, every topic has a source in the Gemara, as I will, G-d willing, elaborate within this book.
Hopefully this helps clarify some of your questions. They are all valid questions and deserve full answers, which is why the Chafetz Chaim mentioned them himself and gives answers that he feels are sufficient.