The phase should be miniscule unless you've got really big distances involved, i.e., how far the guitar mic is from your mouth vs. the vocal mic, are in inches, so I'd be more inclined to think any comb-filtering you are hearing is more likely due to room reflections. Check your treatment, or be careful with FX on the individual tracks. (Yeah, I don't think you'll get satisfactory results trying to Melodyne the vocal track when tracking both together, unless you've really got the ribbons perfect, perhaps, and then maybe standing up to increase the distances.)
You might try doing that first tracking as just a scratch, then go back and do them separately, with the scratch in your monitors. You might be able to keep the feel that way, but then end up with independent tracks that are more malleable. It's what I do when I'm going to be adding more folks in. Sometimes the scratch stays, but a lot of time, it can be replaced by something better when the focus is just on the guitar or vocal.
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