If you don't mind me asking, why are you using such a long lens to try and do macro shots?
I would imagine the minimum focusing distance on the 100-400 would not be particularly close to begin with, and the TC wouldn't be helping either.
Anyhow - even using the 100-400, why don't you try using the lens without the TC? Even if you're shooting at f/8 without it, you should still be getting more light coming through the lens without it (thus shorter exposures), than with it attached...
If anything I would be looking at getting an extension tube to be able to focus closer to the subject to help fill the frame better (instead of using the extra zoom). A 12mm tube lets you focus a fair amount closer, while still being able to focus quite a way out (though not to the horizon), whereas the 25mm tube is a lot more limiting on the far side...
The other thing is that even with the IS of the 100-400mm, if you're shooting on the long end any camera shake (even slight camera "pivoting", ie: the lens swinging aroung slightly as you hold the camera) will be A LOT more noticeable and detrimental to image sharpness working at such short focusing distances.
As a general rule though, I don't think any long zoom lens will give great IQ doing macro shots. I tried using my 70-200mm 2.8 IS mk.II when I had it to do Macro shots, and it was miles of the macro IQ of the 100mm IS L Macro I still have.
I don't know if this is all technically correct (or any of it, lol...), but I shoot quite a bit of macro stuff and that's about all I can think of - Hopefully it's some help!