The most important thing when micing amps is that you have a good sound in the first place. I know that sounds obvious, but you have to take everything into consideration.
I was having a lot of trouble getting a good sound from my guitar cabs also. Same problem: mud, no highs. I have a 5150 II and it just didn't sound right. Then I realized that when I'm on stage or practicing, I'm playing through a full stack and it's totally cranked, and THAT's when it sounds the best. Tube amps especially.
So what I would recommed is that you try EQing your amp and adjusting the volume as if you were going to play a gig in a good-sized club. That way you're driving the tubes and pushing the speakers to where they were built to perform and you get optimum sound. Don't be afraid to record at very high volumes.
I'm also running my mics through a tube preamp, which is DEFINITELY a good investment. Especially when recording a distorted guitar, drive the tubes on the preamp a bit and it just fattens it right up. Tube preamps are also good for warming up digital recordings in general.
I really hope that helps and that I'm not just stating the obvious.