I have a guitar track that can't be repeated (I changed the pickups on the guitar) and there are 2 or 3 digital overs, i.e. transitory nasty crunch/clicks. I've homed in on them and am trying to disguise them with volume drops using volume envelopes for each one. I'm getting some success but haven't managed to totally hide the glitches.  Any tips for the best way of doing this? 

Try to replace whole chords or sections from other sections where it's clean and crossfade them with a short time.

Hi John
 
I guess it's really down to what guitar is actually playing when the glitches occur.
 
You'll have more luck replacing the section as described above if it's rhythm/chord work, but less so if it's an exposed solo.

Izotope RX can fix the clipping. You can also try to edit the wave form in an audio editor like Sound Forge. 

I beleive iZotope has a plug called De-Clip. I'm not sure how well it works, but maybe it's worth looking into.

Depends on how long the overs last. I've successfully fixed some by zooming in to the sample level, copying adjacent non-distorted samples, and pasting them over the ones that clip.

It sounds as though the OP's overs are significantly long, since overs typically only become noticeable when they span hundreds (or thousands) of samples, in which case manual editing isn't practical. If that's the case (as opposed to just finding a handful of overs and fearing they might be audible), then you have just two options: substitution or hiding.
 
In some cases, you can copy-and-paste another bit of the track over the offending bit. Careful crossfading can make it seamless in the mix. If that isn't possible, use the masking effect to your benefit. Use automation to dip those parts and raise something else with a similar frequency signature to cover it. You might even add a new part just for that purpose like a shaker or tambourine. If it's short, a crash cymbal hit might be sufficient to mask it. If not, a short piano run can be made to sound like it's complementing the guitar but in reality is taking over briefly to cover it up.