Ok, So I've got the orthography down, and the proto-sounds.
Fricatives:
/ɸ β f v θ ð s z ʃ ʒ ʂ ʐ ç ʝ x ɣ χ ʁ h ɬ ɮ ɕ ʑ ɧ/
<p b f v t d s z š ž ŝ ẑ ţ ḑ k g ķ ģ h ł l ś ź ḫ>
Affricates:
/pf bv ʈʂ ɖʐ tɕ dʑ tʃ dʒ ts dz/
<ṗ ḃ ṫ ḋ ŧ đ č ǯ c ʒ>
I'm not too happy about ṗḃ ṫḋ, so if anyone's got any alternatives (no digraphs), let me know.
Approximants:
/w j ʍ ɥ/
<m j w y>
Vowels:
/a e i o u/
<a e i o u>
Diphthongs:
acute: Vj
grave: Vw
circumflex: jV
caron: uV
macron: long vowels
Ok, here's the sound changes:
*p b t d k g q ɢ > ɸ β θ ð x ɣ χ ʁ
*pʲ bʲ tʲ dʲ kʲ gʲ > f v ç ʝ ɕ ʑ
*ks/sr gz/zr rs/rk rz/rg > ʃ ʒ ʂ ʐ
*r x sl l sk > h ɬ ɮ ɧ
*s z > s z
*p: b: rt rd q: ɢ: k: g: t: d: > pf bv ʈʂ ɖʐ tɕ dʑ tʃ dʒ ts dz
*m n > w j
*xʷ/kʷ/qʷ gʷ/ɢʷ > ʍ ɥ
*ʔ > Ø (diphthongs)
*VhC > long vowel + C
*VnC VmC > VjC VuC (except maybe *nG (G = velar/uvular))
I will probably come up with more specific rules as I go along. That's what I have for now. Any suggestions are welcome.
