I've not done this, but it sounds interesting. I would think that the signal needed for the plug-in to sound right would be the guitar-in feed, not the Eleven Rack feed that powered the stereo track you already had.
If I were to do this, my first un-educated attempt (aka guess) would be to set up a second stereo trackwith the input as "Guitar In" and then the plug-in first on that track.
As you play and record, you should end up with two stereo tracks. One each for the 11R unit and plug.
Another assumption I would have is that I would make sure that Delay Compensation is turned on. I'd imagine that they would be off a little bit without it and start to sound quite out of sync. If your recording sounds much better than the "live" version, you'd probably be able to assume that it might be a timing (or clocking?) type of issue.
On a side note, you could do this in mono. You could also split to mono afterwards and decide how much or little or what signal goes to which side.
Hopefully some of this helps. Let me know if know dice and I'll give it a whirl. Remember delay comp or I doubt any of it will sound decent.