I think you did an amazing job bringing these “would be” sets to life!
Your speculative choices seem very plausible, especially for the Matoran. Very good point on Nobua and the wizard characters - there are many mask colors and Matoran body part colors in those early games, which we have not ever seen realized, but are present in the parts sheet. We also know both Saffire and Templar studios recieved many prototype sets to use as references and some of them may have had these parts. Medium lime Miru being used on the wizard is very clever and I didn’t even think of that possibiliy 
Also, the fact that purple Hau did exist (and probably still does) makes me even more confident that Nobua has been there all along and was meant to be a prominent character.
I wish they went ahead with violet Macku - she is the only 2001 Matoran with no special color.