Thanks everyone forall the advice and links. I will work on this today.
Regarding the offers to help transcribe or analyze the part: thanks very much, but there are a lot of licks in the song and I would not want anyone working on this without being paid.
I think some of the software recommended here should help. I alos like the suggestion of getting the polyphonic version of melodyne but only running it stand-along until i am sure my Melodyne Assistnat files are safe. (BTW, I run sync toy daily to back up Melodyne files as I am quite paranoid after having lost a lot of work once due to a Melodyne reinstall.)
To clarify: I am planning to recreate the track using RealStrat (MusicLab) and Guitar Rig 4. I already did this to a couple of simple stand-lone lines and was able to match the sound very well. (In fact, the RealStrat+GR version is a little fatter.) If it turns out that I keep some of the original licks and subsitute others, I will change my tone and pan the guitars so it will sound like two players.