I, too, have had very little formal musical education. But there's another reason it's so hard to hear some of the guitar parts on the early R.E.M. albums. Take "Murmur" and "Fables," for instance, where Peter did so many electric and acoustic overdubs that it's difficult to isolate the individual tracks. Joe Boyd, who produced "Fables," once commented that, while usually in the studio each band member wants his or her own parts to be made louder and punchier, everyone in R.E.M. wanted their parts turned down!
As for the Janglebox, I think you'll find that it sounds particularly dramatic with 12-string guitars, but that regardless of what gear you're using, it can take a while to really dial in that "sweet spot." Once you find the right settings on your amp and the pedal, though, you'll hear a quantum leap in tone.
I agree with you that most of the online, so-called tab transcriptions, are wildly oversimplified and not very helpful. I just wish someone would put together an R.E.M. tab book that contains authoritative transcriptions of some of their earlier material. Maybe you and I could collaborate on one, Werner?
Robert
I should pay more attention 
That song sounds really good on a six-string!
