At this point, I would say that Katie is back to being about 90% functional. Part of the decrease has to do with her age (10 years). At some point, you just don't jump as high or feel as stable as you used to. I could see that happening a little prior to the spinal stroke and I think the spinal stroke simply sped up the process.
So back to traveling. I think that some of this caution and fear that developed due to the hind leg weakness has had a residual effect on how she reacts to being jostled or rocked. There were several occasions that I or the vet techs fought with her to make her lie down not realizing that she simply did not want to lie on the left side. At the risk of over analyzing this, I think that sometimes the traveling reminds her of the fear and fight of avoiding the left side and it creates an unhappy experience in the van.
It is uncomfortable to watch her for 3 hours. Most of the time I am driving so I do not see how uncomfortable she appears. She will stand up, turn around, and fluff bedding over and over and over again. Bumps and noises cause worrisome expressions.
I may have to come up with some creative ways to improve the traveling experience for her. Maybe even something like a stuffed Kong or a bully stick each time could make traveling more fun and help Katie to forget the bad experiences. With her intense food motivation, changing her mind is always easiest to accomplish through her stomach.