Hi Fergus,
I've enough experience in this field to help you (as you can check
here
), but as you already suppose, this kind of project may require a lot of custom work ...
LimeSurvey is doing pretty well the data collection part (yes it's its main job) and the token system allows to manage patients. That's a good start.
Extra work is needed for the individual reporting part, so everything depends on your project size & the amount of patients included.
The "nice way to track changes over time" is maybe the most difficult part but would be easier if you can use some scoring system and/or validated rating scale (available in the public domain of course)
I'll send you asap a PM with some resources related with similar projects...
BTW you can also ping @fransmarcelissen (cf
digipsy.nl
) for some related advices or anything else