Hard time with my G string

I have just bought a secondhand Tokai TS-60 Strat (`62 replica), and have a hard time getting the G-string to sound right.
I have intonated the guitar, and when I play with a clean sound it sounds great, but as soon as I add a little distortion it`s getting really muddy.
It`s like when you fret the 5`th on the B and play it along with the open, high E string to tune it, you can hear the vibrations untill you`ve got it tuned right.
The same thing is when I play the G string alone with distortion you can clearly hear some vibration, and it doesn`t matter where on the fretboard i fret, it sounds terrible all over.
Any clues to what I can do to fix this ??

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That`s a problem with every guitar. That third string is a real pain in the ass. I don`t like using the 5th string method becaus it really doesn`t work for me. The only time I use that is when the guitar is way off and I need a point of reference.
Here`s what I do. I tune to simple chords. You use the same method using simple chords as the fifth fret method, you listen for vibration. After you get the high E tuned and you tune using the 5th string method, hold a Dmaj chord. Play the first two strings together. Now start with the E and B string of that chord and tune the B string until you lose the vibration. After the B string is tuned, once again hold the Dmaj simple chord and play the G and B string and tune the thrid string until you once again lose the vibration.
There is no perfect tuned guitar but I found that this method gets it as close as you are going to get. Remeber that weather changes affect your guitar so it`s constantly changing. But anyway, continue tuning your guitar with the Dmaj chord until you run out of notes. Continue tuning the rest of the strings using the Cmaj chord and then the Gmaj chord for the low E. Hope this helps and good luck.

back and deaden the springs with a cloth and see if the springs are the noise makers. If this fixes it, you need to deaden the springs.
What I do is get some 3/16" heat shrink tubing ( http://tinyurl.com/ssgt ) cut it in 2" lengths, split one side of it lengthwise so that it can curl into itself and insert them into the holes of the springs. Once inside the spring, it uncurls and snugs against the inside walls of the spring.
This works better than cloth or cotton because it doesn`t work itself out and there are no fibers that get caught between the coils.

For another option you could try this:
Tune the "G" string 1st, then tune open between "G" & "B". Tune every other string using 5 & 7 harmonics from these.
Note that if your string harmonic cannot be produced "directly" over each fret, the guitar still is incorrectly intonated. (possibly just for that individual string)
If your guitar is properly setup, I would be very intersested in knowing what guage strings you are using. Are they hybrids or ultra lights? Unfortunately this can "heighten" intonation problems.
What XXXRayted said about tuning with simple chords is normally the only way I have found to compensate for the lighter guage strings on my acoustic.
With the guitar being second hand, is there a chance that a previous owner over torqued the truss rod in the neck? This could cause some of the same affect. I would dare say that even if the rod has never been professionally adjusted, it may be time now. In some guitars the rod will move after several years of play, sometimes enough just to mess with the intonation.

through a period where I tuned to a perfect E major chord. Which I came to realize was a good way to guarantee the D major chord would be out-of-tune.