Track, track, track, track, track until you're blue in the face and want to kill something. Track in small sections if need be, edit as you go it's better for you're brain. One thing I've noticed is that if you auto-quantize a riff say using elastic audio in PT, it will detect the pick attack as the transient and thus put it on the grid which makes the guitars sound ever so slightly late. What I've found the quickest is auto-quantizing then going in and just quickly checking / fixing what it didn't do properly then moving on.
Also tuning is just ridiculously important. If you hear something that is even remotely out of tune, retake it. Tune the guitar to the chord / position on the neck the guitarist is playing. A good idea is say if the guitarist is playing a chord progression that uses the 8th, 10th, 5th and 7th fret. Tune to the closest fret to the "middle" of the chord progression so in that case tune to the 7th fret and as long as the guitars intonation isn't COMPLETELY fucked it should stay in tune for each chord.