1. You get to pick which crystal Dorak gives you, but if you're wanting something other than Blue, Yellow, or Green, then you'd need to either edit one of the scripts or add another option to the dialog with a new script.
Blue crystal response uses k_pdan_saber12,
Yellow crystal response uses k_pdan_saber14,
Green crystal response uses k_pdan_saber13.
These scripts can be found in the dan13_s.rim in KotOR Tool.
2. You would need to edit the k_pdan_cryst01, k_pdan_cryst13, k_pdan_cryst14, k_pdan_cryst15, k_pdan_cryst16, and k_pdan_cryst17 scripts in the danm14ae_s.rim in KotOR Tool.
3. That would depend on the level, but you could look for a .uti file or something in the level, or try looking at the level's On-Enter script...
You will need DeNCS to decompile the scripts. DeNCS should be on starwarsknights.com.