I'd definitely call Aquarium Products (call weekdays before 4:30pm) at 1-800-368-2507 about the rocks and plants. It is likely to stain your silicone though. It may kill any plants too...it destroyed any trace of algae for my pleco in my quarantine tank.
Clout is a very aggressive medication that contains Malachite Green. While it seemed harmless when I treated my haps with it for a form a bloat I'd be greatly concerned with using it for Tropheus which to my understanding are very sensitive to water quality.
If you do decide to use it though I'd keep a very close eye to on the Tropheus and their reactions to the meds (do major water changes if they show signs of stress) and water quality (setup a spongefilter or borrow media later after treatment to regain lost bacteria. My quarantine lost maybe 80% of its bacteria during treatment.) since clout will disrupt the biofilter. You could also keep overdosing Prime daily or dose ChlorAmX to detoxify any ammonia and nitrite.
Lastly, it would probably be best to feed metro soaked food for a while and treat the water column with metro 1-3 times daily. Metro is harmless to plants and ime is harmless to healthy fish.
Just remember, if Kim (cichlidaholic) or Robin say any treatment things different than me, LISTEN TO THEM NOT ME! I have ZERO experience with Tropheus and while Metro never worked for my haps (there are so many causes of "bloat", the one plaguing me is different than the common Tropheus version) I hear it works wonders for Tropheus and that Clout kills more than it saves with Tropheus. I'd only use Clout as your last option as I did.
I hope any of that helps...