One last bump here. I had run into some personal issues that cut out most of my "SH3 time" that appear to be mostly resolved.
It seems that quite a few of you have figured out or already knew how to fix individual paint schemes for non-reflective Type II and Type IX sub problems.
If you would like me to fix further skins let me know and I'll be happy to do it for you.
Otherwise, the instructions on how to do it are in this thread.
Cheers! Mates you all rock!