Story XP - works fine, but I've made a custom option that works better.
Fear and Horror - only came up once, in the Lost Temple of Tharizdun. It was pretty fun, giving the adventure an edgier feel.
Hitting Cover - in theory, this is cool. In practice, unless the cover is another monster, it doesn't matter. PCs generally have higher AC, so the "hit" on the cover becomes a miss.
Injuries - bad. bad, bad, bad. Maybe for a one shot, but it quickly makes PCs into walking/crawling wrecks. I'd suggest avoiding it.
Morale - I've used it, but I don't like it. It feels like Wisdom isn't the right ability (maybe Cha of the leader?), but I haven't found a better option. It works well enough, until I can figure out a better method.