After much ripping and knitting and ripping again, I think I have come to peace with this yarn and its fugitive dye. I have completed the front and back of the sweater and sewed the shoulder seams (although I did skip the blocking step).
Avoiding any unforeseen complications this sweater should be finished shortly. I did some calculations and while the NAKNISWEMO usually assumes 50,000 stitches and this sweater has closer to 40,000, I think I have more than made up for it by knitting large sections of it twice to avoid faded yarn and knotted skeins that ended in unfortunate places.
Now I am off for an early version of cookie Saturday.