I've figured out how to use Moodle's jquery and jquery-ui, rather than include the source for both within the Parson's problem prototype. This reduces the HTML size from around 300k to 14k! It also removes potential conflicts between the two different versions.
I've also fixed the bug that allowed you to lose lines by dragging them off to the right of the window.
The updated prototype can be downloaded from github: https://github.com/trampgeek/ucquestiontypes.