I guess this forum really isn't set up for the kind of intense assistance & interaction you really need. Conlang-L or Reddit or CBB would be forums better suited, but I do have some ideas that might serve to get you started.
Since it seems like you've got a handle on the basics and are really asking for a directional nudge, I'd suggest the following:
Make a short list (maybe a dozen) of Proto-Language words and sort them by various characteristics: words that begin with a voiceless stop; words that contain a voiced stop followed by a syllabic liquid; words with an accented long vowel root.
Pronounce one of the words over and over and try "permutations in the phonetic neighbourhood" like CWADRUT CWADRUT CHWADRUT CHWADHRUT CHWAAHRUTH HWAARRUS HWAARUH HAWARƏH HAWWAR
Make a note of how certain sounds are "eroded" or, I guess more properly, how they evolve. [kw] relaxes into [hw]; [dr] > [ðr] > [r]; as the final syllable weakens, the accent shifts towards the word head; as the accent shifts towards the word head, medial long vowels become shortened.
Sit back in astoundment how you've just discovered several sound change rules!
If you don't like that progression, try another one.
Kind of a simplistic exercise, but it's a good method to start. Eventually, other rules you discover are going to intersect and sometimes abrogate another law. Sometimes two parallel dialects run along slightly different tracks.
Sometimes dialects are "behind the times" when compared to others, and this will launch you into the wonder world of diachronics. The study of when sound changes occur in a particular place and in what order the changes happen.
And of course, you're considering a whole family tree, so you're going to need to do this exercise multiple times. You might find that two or three daughter lineages kind of align in certain ways. For example, *cwadrut yields hawar in language A and qewarro in language B and kawrs in language C but shwuntz in language D and shhwandaras in language E.
As you examine other words, you notice that ancestral [k-] remains [k] or becomes [h] (both palatal sounds) in several languages, all of which are at the eastern end of this proto language's continuum; while most of the languages where ancestral [k-] has become [ʃ] are all in the west. A nice geographic split (that may or may not actually mean much), much like that which exists within Indo-European languages.