Hi again,  just mixing a new tune of mine, and finding my clean guitar track/main lick is "warbling" a bit against what seems to be the bass track. It may be the sum of the bass and drums and is subtle, but noticeable to my ear anyways. I'm having trouble finding exactly where the trouble is, and how to eliminate the problem interaction. 
1) Would you possibly be able to tell me how you would approach this sort of problem exactly, step by step?  Which tools exactly would you use?  I  just have whatever comes with Sonar Studio X3. 
2) How do you approach cleaning up / thinning out the mix so that it's not losing anything as far as quality of sound goes, but thins out the areas that seem a little too muddy or full? Looking for a very clean distinct yet full bodied end product. Not asking much for a newbie, huh? 
 
Appreciate all the help!

Hi. I would probably try using subtractive eq ,to separate the tracks in question. Bass and guitar share some frequencies that could make you hear the "warbling". Others may know better.
Best of luck.

If you suspect frequencies are competing and your ears aren't helping you to find the problem, you can try a visual approach.
The QuadCurve or similar EQ will show you the full frequency spectrum of the signal being fed into it. Place an instance on each of your two tracks and look for the frequencies they have in common. Decide which instrument deserves that area of the spectrum and cut the other one by dialing in the Freq & Q and subtracting a few decibels. Keep the Q reasonably wide so you don't end up with surgical artifacts in the neighboring frequencies, but not so wide that you deaden the sound.
If the problem lies at the top end of the bass, and the low end of the guitar, you probably should just roll-off the frequencies above and below a certain threshold, as Zargg suggested. 

Voxengo Span can help here.
 
You can set it to show 2 simultaneous displays, for example Kick & Bass.
 
From this you should be able to identify if anything needs complementary EQ and clear space for each other to breathe.
 
 

Wavefactory's TrackSpacer.
 
The easy but not cheap way of doing it.
 
You'll get no engineering degree from using it, but it can do the job nicely.

Voxengo's GlissEQ has been the "go to" for this kinda of thing.  You put an instance of this plug in each track that you suspect is fighting with one another.  You can then display the spectrum of all those tracks (up to four at once, I think) simultaneously and see where the tracks are overlapping, and...(since it's an EQ and all)...you have the tool to do something about it right there.
 
I've also heard good things about some of Melda's tools like MMultiAnalyzer...
http://www.meldaproduction.com/plugins/product.php?id=MMultiAnalyzer
...but I don't have any direct experience with their stuff.
They also have a thing called MSpectralDynamics, which goes a few steps further than this...and appears to be so flexible that it's pretty downright scary.

For me, MMultiAnalyser from Melda Productions tops the lot. Currently €59 / $65, although there are discount periods from time to time. 
 

A little confused by your mentioning "warbling." Do you have any compression on the master bus?

Anderton
A little confused by your mentioning "warbling." Do you have any compression on the master bus?

Nothing on the master bus...  it's almost like a tremolo effect, kinda hard to hear, but subtly there. Comes out more prominently after converting to mp3 as well. 

Is it a slow cycle, like a phasing or comb-filtering sound, or is it fast?
 
I'm guessing you know what beats sound like when two sounds are slightly out of tune, right?  That's another thought.
 
Can you solo two sounds and hear it?