Yea, I don't think poisoning Yuslan Sha'Rim would be really working as you explained, that would be an easy task for the high ones to work around.
The idea of some Pyrean documents sounds really awesome and can be very convincing, I bet Arantheal may feel a bit offended since it may tickle his pride in some way hehe. A great time to place that document could be around the time of the Aged Man quest of Old Dotholgard ruins (the place that Calia revealed her demon form killing the bandit leader) and the beacon was discovered, or may be that first temple (maybe that's older than the Pyrean civilization?) One challenging thing is to make the document look real, could be language issues and archaeological dating, or may be a few of them has to be placed in different places.
Lijam's rant at the tavern sounds a really good idea hehehe and great observation you took about he may not like the upper management. I like the idea of 4-person safe-proofing the beacon, and a betrayal-proof too! If someone tries to light the beacon alone without the Numinos, that person should be killed whether it's a teammate, superior, or Arantheal.
One thing that I noticed that's kind of a gap about Lishari's murder, if she feels that someone was going to take her life that bad (while making appointment to see the prophet at the Dancing Nomad), she should've asked the prophet or whoever she trusts to accompany her all the time, or keeping a close distance, something around that.