Hi there dlotto.
The muddiness of several of the models is a frustrating obstacle in the HD units, but it's not entirely impossible to overcome. I've found that there are two approaches that work well for me.
1) Place a graphic EQ in front of the amp model. First cut 80Hz by -3 to -6, then cut 220Hz by -1.5 to -3. This should help remove some of the muck from the tone, and allow your articulation to be better pronounced (esp. through distortion).
or
2) Use a screamer model before the amp model. Turn the Drive all the way down, set the Level to about 70 (where I feel it's neutral in terms of output level compared to the Screamer being bypassed), and then toy with the tone knob to taste. The Screamer model will shape the tone by filtering out the lows responsible for flubby atriculation, but will also shave off some of the high end, leaving a sound that's neither muddy nor very shrill/shimmering.
Bonus idea (since I just thought of it lol):
Use the Mid-Focus EQ before the amp model. First, turn the Gain all the way down on it. This will make it's output gain neutral, and keep it from acting as a boost. Next, set HP Freq to 0, HP Q to 50, LP Freq to 100, and LP Q to 50. Finally, play something that requires your tone to be more articulate (I find setting the looper to play before the amp to be helpful, as you can let the looper play for you while you tweak). While playing, creep the HP Freq up until you notice that things sound more articulate. This is once again hammering down the low frequencies from your guitar which the HD translates as mud.
Well, that's all I got. I hope that it proves helpful to you. Good luck! :)