Great work zwilorg!
---------- Post added at 06:22 ---------- Previous post was at 06:18 ----------
I think that you use D5 for protection, but it's not needed. because each of analog pin have two clamping diodes that clamp any voltage above Vdd to about Vdd+0.3, and any voltage below Vss to about Vss-0.3.
---------- Post added at 06:26 ---------- Previous post was at 06:22 ----------
Also i think that you used C1 for stabling. but it's value is very large and can slow down measuring response. decrease it to less than 1uf (or even less than 0.1uf).
---------- Post added at 06:34 ---------- Previous post was at 06:26 ----------
You should decrease R11 to less than 2.5K (while keeping the ratio of R11 to R12 constant, for correct voltage dividing). it should be decreased to measuring more accurate values (for more information see "Analog to Digital converter" section of datasheet of your microcontroller).
---------- Post added at 06:42 ---------- Previous post was at 06:34 ----------
If you want to measure hot junction temperature with less errors:
-->Use 1% (or less) resistor for R11 and R12.
-->Use an external voltage reference for your AD converter (such as LM336-5)
-->Follow the recommendation in AD595 app notes.