I would powershell into the device and start digging around. First, I would use the iotstartup command (don't remember which options) to find out if the application is installed. If it is, I would look at the wevtutil logs (again, can't remember options) to find out if and why the application is starting up and/or having problems.
For our FFU, we are not using the EV certificate. It is used during the build of our UWP application for signing that, but not used by the FFU. We let the FFU generation to self-sign the custom packages we build. At no part of my build process do I use our EV cert, as a matter of fact it is not even installed on the machine that does the FFU generation. I would consider not using an EV cert during the generation process at all.