Thanks, it was quite an ordeal.
I actually shifted the guitars to match eachother phase-wise after recording. There was a slight difference on time, but it wasn't too hard to fix.
Reaper is awesome, I can send you some good resources for working with it. It's also FREE (or $60 for the full version). I love it. I think it's a lot like pro tools, but its the only DAW I've used, so idk if thats true.