I have an idea that the custom Nav (that currently does not work in the publish environment) is causing an issue leading to excess render time (not loading time). I am planning to make a new version of the app that does not have this feature to see what impact that has on the speed. I cannot do that until Monday however when I am back in the office with my developers.
Because these are migrated folios and not folios created with the new set of API's for Publish then I know they may not be optimised as well as they can be. However for various reasons (namely cost and time) we are unable to integrate our CMS with new workflow for at least six months. The publishing plan for now is to continue to Publish via DPS classic and then migrate those folios into the new environment (does that make sense?).