You have to keep in mind that a mic is going to pick up sound in a different way than the human ear. Settings on an amp that work well for live use, usually are not the settings that work best in a recording situation. Playing around with the gain controls(too much distortion kills tone and clarity) and equalizer might work.
Also, you're using a large diaphragm condensor mic, which can start distorting when subjected to a lot of low end and high pressure levels. I would try placing the mic at different distances from the driver, and see if putting it farther away makes it sounds better.
If you happen to have one, I'd try using a dynamic mic such as the Shure SM57 in stead, this is a more common way of recording distorted guitar.
That's about all I can come up with for now, hope it helps.