I see this thread took a right hand turn away from EQing, but I will still comment on the original post title.
What everyone else has told you is true. If you have a short (standard) scale length like 25.5" or so, you are going to have major issues with tension.
Also, what kind of tremolo do you use? Just curious.
Ok, and as far as EQing to get rid of the "mudiness"........
This may seem a little tedious, but I've found it to be the BEST way for finding desired EQ settings. Now, you already said that your mids/lows/highs are all pretty much cranked, and you were going to try turning them back to see if it helps. Well, IMO, you are approaching this totally backwards.
What you SHOULD do is.....turn ALL your settings to ZERO. Gain, volume everything. Now turn the volume knob up to a reasonable value (something you would normally use with your old settings). Turn the gain up, little by little, carefully playing and listening to how the gain affects the overall tone and clarity of the sound. Find something that sounds like the right amount of gain, then turn it back a notch. Approach the low/mids/high this same way, doing one at a time, slowly adding low/mid/high until you find something that sounds right. You should see, it will sound like it's getting closer and closer to what you WANT, and then at some point it will start to go away from what you want. Now turn back to the point where it changes. After you've set your EQ's, I recommend going back and re-doing the gain setting. Do it the same way, starting over from zero again. The values of the tone could GREATLY influence your opinion on a gain setting.