Thanks for the correction, Si, although I'd be interested to know where you got your information about McGuinn's first Ric. I was under the impression that all of the information in the Guitar Player article came directly from McGuinn. I think it's highly unlikely that whoever wrote the article was doing guesswork on McGuinn's gear based on his tone on that first record. After all, the author also mentions McGuinn's use of the exact thumbpick/fingerpick arrangement you noted, not to mention Roger's preference for the bridge pickup and other assorted tips. Keep in mind that McGuinn was still an acoustic 12-string player when he purchased his first Ric, and that he was definitely accustomed to the traditional stringing. Thus it wouldn't have seemed such a shock if he reversed the octaves when he replaced the nut on that guitar. Listen to the intro and outro to "Mr. Tambourine Man," and you can clearly hear downstrokes on the D and G pairs (not to mention the high octave strings being struck before the fundamentals).
The traditional low/high Rickenbacker string configuration has become a huge part of McGuinn's tone, but not from the beginning. I would argue that sometime between the albums "Mr. Tambourine Man" and "Fifth Dimension" McGuinn reverted to Ric-style stringing and altered his approach to the instrument. To my ears "Eight Miles High" was definitely recorded with a 360/12 strung factory stock.
