Anderton
This probably isn't the answer you want to hear, but for fixing timing on guitar parts I use AudioSnap and it is fantastic in that application - quick, effective, and straightforward - but only once you get past the user-hostile learning curve. I really need to do a video so people can see how easy it is...
Actually, I'm hopeful you will do a video so that I can use AudioSnap. You're correct, it is a user-hostile learning curve that stumps me every time. I'm open for anything that gets the job done correctly and easily.
Oddly, I've used Melodyne to fix the timing of a bass track with great success. The timing gets fixed, not artifacts and no weird sounding phase issues. I'll have to try some of the other algorithms available in Melodyne to see if that makes a difference.