I assure you that a blacked out theme will have problems with system text colors.
yup
Whether you use Stylebuilder or SKS your going to run into problems trying to make a totally black theme, its just not possible to cover all the text options in windows, that aside, many applications also use hard coded text, usually black, The half baked'ness you talk about is caused by this. NT is correct, nothing you can do to get around it. period. Skinstudio however does give you more options to change most of the text colors in windows. In a visual style as far as i can recall you will have to change it from the display properties dialog but it will not change all the text and wont cover third party applications.
I've used both Stylebuilder and Skinstudio and I can assure you SKS gives you a better chance of getting close to pulling off what your trying to do. I wouldn't however recommend using both on the same system.