If I want to capture the feel of a tune on acoustic guitar I record it as it is … not against a click track or anything else, the acoustic recording becomes the “master” as far as timing is concerned. If that’s not good enough then accept reality – it’s simply not good enough, and you need to practice more. Nevertheless it is difficult to do everything perfectly on a single take, and what you might get away with live is often not acceptable on a recording.
Kwackman’s suggestion above is a good workflow, but investigate “Working with Lanes” in the manual; I would suggest playing the piece through in several takes, and then using Lanes to comp the final track, rather than section by section, but you’ll have to figure out something to use as a timing reference. As you’re both performing and engineering the recording, this will actually be easier and more effective than if you were trying to direct a musician. It takes a little time to master, but it’s well worth it.