Sending stuff to your battle tower shouldn't have been a problem. I was thinking that if you left the loot bag from Stone there, maybe grabbing it would update something (if you picked Igor as your necromancer Stone will drop a ring he wants for one of the platform quests).
The gates in the arena can not be opened (presumably they are the cages where the rest of the opponents you faced were kept).
I also used the first 4 invoker jewels in the headquarters, before finding out there was a fifth in the arena. Using all 5 together produces a chest (with random loot), in addition to stopping the machine.
Since you finished Stone's flying fortress, you are a high enough level that clearing the start of the waterfall cave (to get the seeds quest) should be easy. That should reset your dragon stone.
