Impressive setup you have there. Regarding the FHEM integration you probably have missed the fhem-skill (disclaimer: i am the author of the fhem-skill)
Unfortunately Logitech Harmony does not provide a really open API. You might want to look in one of the “wifi ir blaster” projects, e.g. https://github.com/enc-X/mqtt-ir-transceiver which can be integrated with your favorite home automation system.