Also, for some reason, the Ironflesh skill is not selectable. Don't know what that's about.
There's an issue in M&B 1.011 where if you disable a skill in module_skills, some other skills will become unclickable. In a mod of that I was working on, we encountered the same issue when we disabled power draw and the shield skill - ironflesh and power strike became unclickable. I'd check if you've disabled any skills from module_skills.py
Anyways, here's some bugs:
River vertex on map is a bit too high. There also seems to be a patrol stuck there.

Default leggings show through the blue haramaki-do. (leather) I think it's caused by the lack of a itp_covers_legs flag on the armor.

Player party's name string doesn't show correctly:

String error in quest title and description. It's the quest you get when you formally introduce yourself to Hosokawa or Yamana as a Kuge.

Random mission template error during a battle - happened right after I killed a bandit with a dart.

Dialog error upon talking to the letter of introduction guy.

Nearby bridge joined the battle on my side:

The arrow quiver can obstruct first person mode and can clip through the head. I'm not sure if it's feasible or important to fix this one, but AFAIK, the itcf_carry_quiver_back_right seems to be rigged to the hips and tends to wiggle around a bit. It might be possible to alleviate this problem by translating the mesh to fit with itcf_carry_quiver_back, I think.

- The Kuge-introduction quest where I am supposed to deliver a message to Hosokawa Sadatomo also seems to be unfinishable. That may be related to the dialogue error.
- The music also doesn't seem to be playing for me. Maybe the music is missing the mtf_module_track flag?
- Also, I think that the white hair for troops is caused by the limit_hair_colors = 0 in module.ini. In Native, the value is set to 1 and the hair colors are limited based on entries in module_skins.py. My character's hair turned white when I pressed the "randomize face" button.
Additional information: latest version, 0.6.6-b3725. Hope that was some help.