Your Wiki is much too big, much too different, for me to help. I am not familiar enough with it, and I can't find things where I expect them to be. It is overwhelming to pinpoint a problem with one thing when facing the whole guacamole.
Very pretty wiki, but it is too tall a task for me to disect it. Maybe somebody else with the time and the energy can dig into it.
Might I suggest that before you introduce functionality into the big/wildly different wiki, that you try new intended features in a small and dedicated TiddlyWiki instance for that one feature.
So that targettetted unit/functional testing can be done for that feature in isolation, or at most with those artifacts (design elements) directly linked to the feature (i.e. things directly linked to the specific feature).
When the feature is working in the small-scale vanilla TiddlyWiki, then integrate that new feature into the big one, and then do the big integration testing. If what was working in the small TiddlyWiki doesn't work in the big TiddlyWiki, then that helps narrow down the problem.