2. Record drums to the guitar track.
I think I'm just having trouble wrapping my head around this. Is the drummer recording to the guitar track only (without the click)? If so, it would be a miracle if he could follow just the guitar track and still be able to maintain the same sense of feel that the band achieves live, when the guitar would normally be following the feel of the drums.
If you feel the need to alter the timing of the drums, maybe you could do a tempo map (as Silvas suggested) then tighten up the drums, then re-track the reference acoustic to lock it back in to the new groove of the drums. Moving of the timing of the drums will inevitably skew the feel of the reference guitar track in relation to the drums. Been there... done that!
Pro Tools has some great quantizing tools for elastic that allow you to quantize audio by a user defined percentage, instead of snapping everything to an absolute grid. You can also exclude quantizing (by a certain percentage) on events that are already close to your grid. I use these features all of the time to maintain 'relative feel' while tightening up the performance of a 'not so tight' drummer.
I like to map the tempo by identifying the first beat of every bar, then "loosely" quantize (as explained above) the drums to 8th notes or 16th notes depending on what the drums are doing.
The problem is when overdubbing all the other rhythm section instruments, although aligned to the click, the "groove" just doesn't feel as good as when they all play at together at the same time.
Aligning all the other rhythm section instruments to the click is possibly doing more harm than good. The drummer played to a guitar track reference... not to the click (if I'm understanding you correctly). Once again, back to 2 degrees of separation.
The drummer is very good
In that case, I wouldn't alter the timing (or feel) of his tracks at all. Once again, maybe you could try re-tracking the guitar after
the drums are already recorded which would approximate what's really going on when they're playing together.