I got perfectly what you mean... It was a royal pain in the rear to make some stuff correct, I needed to look at Rei's own modification so that I could guide myself... In the end it doesn't look too bad I think. To be honest this was literally my first time at 3D modeling (Blender seems pretty simple to use too), I have a bit more experience with Photoshop but nothing special.
Just to mess about I changed her hair and eye color , removed the shadow that the frills cast on the shorts and the shadow that the waist bag casts on the top.
Also, using NTRs LayeredFS plugin makes trying out stuff A LOT easier and faster than to having to rebuild the whole romfs and dumping nearly 2GB worth of data into the SD card every time I changed something.