Wow, crochet? I love knitting and crochet-ing too! You are very creative if you really do crochet-ing Inuyasha's character! I can only imagine how difficult it is to crochet-ing the eyes part...
Well, whatbher eyes color is up to you, dear! What color did you prefer the most and what color did suit Kagome the most? Well, personally I prefer blue for her.. it's more unique and to me, it feels more like she is 'the special one' with them blue (because there is no blue eyes for pure East Asian). So I did have little resentment with how the anime change her eyes color.. But if you prefer brown, then it's fine...
Hmm..his marks.. Again, there is difference between anime and manga. In the manga, he has them in his face only, but in the anime he has them in his wrists too (but after he got his new left hand, there's no marks in his new left wrist). For hips and ankles..I never see them, because from what I saw (CMIIW), he never shown his bare hips and ankles.. Maybe it just some of creative imagination from most of our beloved author here to add them, to add more sexiness to Sesshoumaru..