I know this isn't as in-depth an answer as you were hoping for, but I found something in the ArtScroll Mesorah Series book, Kaddish, which may point you in a useful search direction. (Kaddish, Mesorah Publications, LTD, Brooklyn, NY, 1980, Scherman & Zlotowitz, eds.)
1.Regarding the use of the word ואראע a comment on page 55 says the Rambam did not include the word וארעא and that the Avodas Yisrael says not including it is the correct version. However, the Abudraham's text reads as מרא שמיא וארעא and that the Emek Brachah says that the version we see that reads אבוהון די בשמיא וארעא is a combination of the texts of the Rambam and the Abudraham.
2.Regarding the inclusion of the word טובים a comment on page 46 simply notes that it is included in Nusach Sfard.
3.Regarding the inclusion of ברחמיו there is a lengthy comment on page 47 that notes that the Rambam and Nusach Sfard both include it, but Nusach Ashkenaz only includes it in Kaddish D'Rabbanan. The Emek Brachah suggests the reason for including it may come from Bavli Sota 49a where it says world survival depends on kaddish, and therefore an extra appeal for mercy is warrented here.