And another user rid of obnoxious Chinese root! Glad to hear it.
Unfortunately, we have a locked bootloader, so a direct flash is out of the question. We need a 2nd-init style recovery, but one doesn't exist for us yet, so we have no recovery option. Worse, I've not been able to get fastboot working either, so it's fairly easy to brick these when you start messing around a little more in-depth. Flashfire also doesn't work, sadly. I sent relevant data to see if we can get support, but don't hold your breath.
Xposed works fine, and if a module bootloops, its disable works too - mash on a volume key while powering on, it'll start to vibrate on press. Keep mashing until you get a longer vibe and it'll disable itself and boot. Disable the offending mod and tell it to install again.
Pushing apps to /system is fine, but be wary deleting them, a factory reset doesn't restore /system and some things are critical for first boot. You'll keep the su binary on factory reset, but to save hassle, install SuperSU as a system app and you won't need to reinstall it from the market on reset.
Custom play stores are fine to install, as are the usual questionable xposed modules, busybox, and similar. Feel free to ask about other mods, I can probably answer.
On the good news side of things, I was gifted a much nicer Xperia Z when a friend saw what I was using. It's now my daily, and I can get much more reckless with the Fierce 2, since I'm not out much if it bricks. I'll be attempting a recovery build with the chargemon unit hook over the next few weeks. These work well on other locked bootloader devices. Not my first recovery build, but it will be my first hooking init, so no promises. I'll update a new thread if anything looks promising.