So the lead guitarist in my band is an insanely good player. He plays with a lot of feel, can do everything from fingerpicking to crazy sweeps, but has a huge problem with timing. Hes accidentally played entire solo's one beat off time, comes in at the wrong time with certain parts, has trouble coming in during parts with complex rhythms, and had trouble getting his harmonies to line up with mine on our recordings.

He is constantly practicing to a click, and has been jamming with different drummers for years. We always tell him to listen to the drums when he plays but it's like he cant "feel" the beat the right way. Weve tried almost everything to get him to have better timing. How do we fix this?
Sounds like he can't groove. Have him play to simple beats with simple melodies whether it's improv or written. He can play faster stuff once he gets the groove for basic things. You have to learn to groove to the beat or fall in the groove. Steve Vai had the same problem except it was mostly in time. Frank Zappa told him the same thing I'm telling you.

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Get him to play Paranoid by Black Sabbath, it's a fast song with a steady rhythm.
He probably needs to go back to basics and build his rhythmic awareness up. Practicing to a drum machine would help but I really think he needs the guidance of a teacher to make sure he's doing it right. Like you say he practices all the time to a click but he may not even be playing in time to the click.
If you are any good you'll be able to help him at your band rehearsals. Get a groove going and make up some exercises that'll help.