I mentioned this on the flightsim.to page for the RCAF MB-339, but I solved all of my model/pilot issues by removing all references to the model in the repaint folder and just using the textures, since the latest patch resolved the issues with repaints requiring model folders in the package.
In summary: Deleted model.JK_RCAF, updated aircraft.cfg to point to default model (model="") and updated the layout.json file to reflect the changes that I made. Back to working as it should.
Thanks again to jankees for the great RCAF paint.