Glad you're enjoying the pattern, David. It does look fun, and it makes such a nice looking scarf.
Yeah, that's the problem with stripes--you have to do something with the yarn when you're not knitting with it. I can only think of two ways to deal with it: either carry the unused yarn up the side or cut it and weave in the ends. I would think that weaving in the ends would be less messy and less noticeable but much more of a pain in the neck.
I wonder if you could convert this pattern to in the round and still have it come out looking like the original but "double-sided" so to speak.
Anywho, perhaps someone with more knowledge can point you to a better solution!