The short answers are yes, I wound the two colors as a pair. It was my first attempt at winding two colors and it didn't go very well. There were all kinds of problems, the impact of which I didn't fully understand until I started weaving. I thought I could write-off the sequence error as a "design element," but it's bugging me and I want to fix it. Knowing how to do so seems like a skill I'll need in the future.
I inventoried the section with the mistakes. Going from right-to-left (direction of the threading) the first pair is correct. Pairs 2, 3, 4, 5, and 10 are reversed. It looks like all are correct coming over the back beam. I'm hopeful that fixing pair 2 will make pair 3 okay and likewise pairs 4 and 5. I plan to finish one pair before starting the next pair to take advantage of the likelihood that a fix to one pair will "fix" the pair next to it.
a. Weave a little extra separator space between the finished towels and the area where I'm going to make the fix.
b. Tie a piece of contrasting thread across the top of the reed dent that has the first thread that needs to be fixed so I can locate it easily.
2. Cut the two threads for the first pair (pair #2).
3. Do a "broken warp thread" fix to each of the threads (I need to review the video and my notes first!), then re-thread the heddles and reed.
4. Check my work from the front of the loom before proceeding to the next pair.
5. Determine if the next pair needs to be fixed.
a. If it's OK, check the following pair.
b. If it's not OK, fix it.
6. Continue until all five pairs are in the correct color sequence and the warp is once again ready for weaving.
Does that sound reasonable?
Before I jump into making the changes, I'm going to weave an extra couple inches of separator between the second towel and where I start the fixes.