In reply tomastering is bollocks, should only take an hour. It's the perfect EQ work you wanna aim for
this is something i've been heavily concentrating on for about 6 months, after having similar problems with EQ and muddy mixes, spending hours trying to 'polish a turd' (the expression is SO true)
The formula i work to now is pretty consistent with all tracks, unless i really have to use a different method. I obviously eq every sound, compress the percussion, kicks, bass and vocals where needed and use limiters/maximisers for the riffs/ riff type sounds. I always used to use compression on riffs but now i find that with the right EQ and a limiter/maximiser i get cleaner results.
Adam, are you looking at a waveform for each sound? you can clearly see which frequencies are clashing this way and EQ accordingly.I've found out recently that voxengo gliss EQ actually shows you the waveform as you eq, and you can overlay 16 other waveforms so you can see exactly how you are shaping your overall mix. Voxengo warmifier is also good to get your sounds nice and tight and crisp.
Run a stereo imager on every channel to see if you have phase problems, correct those otherwise your loosing your music down a black hole!
try to eq out the 800hz region of many sounds except the bass, this helps the bass to stay clear in the mix (still one of the best tips i know!)
try to get your master channel peaking at -5db so you can bump it up at the mastering stage
When you get to the mastering stage..........capture a waveform of your favourite track, something very well produced. Then compare that to your tunes waveform. Aim to get your track the same 'shape' this way you know you've got the right amount of bass, mid and hi's. Then it's just a question of using a 'preset 
' on my mastering plugin and tweaking untill its spot on.
thats the longest reply i've ever written 
Bit ott to me but everyone has there methods to acheive ''their' perfection. and i say ''their'' because one persons perfection might not be anothers which is why this 'skill' is like choosing monitors.
after working with and watchine top enginners...well i should say, experienced, as it more the fact they have been doing it successfully for years for top known artists...so their discography speaks for itself...i noticed that they all do things differently but try to acheive the same, a nice consistant clear punchy mix, obviously dependant on the music style.
Practice makes perfect, and knowledge is power, so learn the tools of the trade then have a play until you get the right sound.
Mastering isnt bollox as it was a single mans job but this as i said was to prepare the mixes for finiky media like Vinyl which needed to be mastered a certain way for optimum sound and signal to noise etc... we dont have that problem but one thing i DID notice is when compressing to MP3 quality drops visually on an audio wav nearly ennough to compress again.
so, Mixdowns is the issue here, master this and you master your mixes...no pun intended lol
you are right however on frequency clashes but over EQ and you could lose the needed harmonics on a particular sound...some clashin is favourable to obtain the 'full' sound.
Kicks - as we are starting to use more samples here a lot of them are 'dirty' with tail ends being noisey... subtle gating and hard compression can sort this...but be careful you dont numb the overall sound too much... 2-3 kick layers should do it...maybe send all to a group channel and globally compress and clean.
Bass - MONO is the key for lower as is for a kick, but some Mid sounding basses can be stereo for effect when putting through delays or fattening through a chorus or phaser...EQ is your friend here too as clashing basses can cause canellation.
As for the rest....crisp top end and noticalble Mid.
and just add your dynamic effects for your final mix to your main outs.