Well, it would have been faster to just attach the TIM files
Anyway, if these are all the variations you've found, I can see the only cases that have text for both CLUTs are the ones with white on black, which reduces the number of special cases I have to take into account.
I'll get to work on this tomorrow. I think I can have it ready for the night, unless something comes up.
As a fun note, if you open a TIM file that doesn't use the second CLUT to display text (like the one with black on teal) in a hex editor, you'll find that the part of the header that contains the palette has some sort of path written on it. That is, what seems to be random colours in the CLUT is actually text. For example, the one in 04.png reads as "1.005\BIN\MSWIN3~1;C:PE" after the four initial white colours. Even part of the first CLUT is used that way. This is one of the reasons why keeping the headers intact is important (because who knows if that's actually used for something...).
I had forgotten I have the BPB files myself too. I took a look at them and it seems the two layer trick is used for the three colour sets, so I updated the Text Editor with the option to use the CLUTs that would be used in the TIMs with two layers. It's just a couple of checkbuttons under the text area, check the leftmost one to have what would be index 1 and then the rightmost to get what would be index 2.https://dl.dropboxusercontent.com/u/144016034/AC3_Text_Editor_1.3.jar
And here's the little program to merge single-layered TIMs into a double-layered one:https://dl.dropboxusercontent.com/u/144016034/AC3%20Layer%20Merger%20v1.0.zip
That being said, it's not all good news. Apparently I've done something really wrong with the CLUTs in the Text Editor. If you choose the CLUT for the secondary layer in a "white text on black" texture, the background is shown as blue, even though it's not a colour in the CLUT
If I convert BMPs made with it using TimView+, the CLUTs are okay... for the first 4 colours. The rest are something else (which would explain why I'm getting that blue out of nowhere). This *might* not be as bad as it sounds, since there's still the step of replacing the header, which I haven't tried.
So here's a bit of homework for you:
1) Turns out I don't know how to extract 4-bit BMPs from TIMs, so please get a double-layered one, extract its "layers" and turn them into two separate one-layered TIMs *without* editing them. Now merge them with the Layer Merger and open the resulting TIM. If it looks like what it was originally, the Layer Merger is the best thing ever. If it does funny things, please show me (send me the TIMs you created).
2) Now edit those BMPs with the Text Editor, transform thsoe into TIMs, merge them AND replace the header with the original. Let's see what that does.