Well I did some more reading and I think I narrowed my story down a bit for them. I think I'm going to go with a story revolving around a master shedim who either:
a) Takes over the body of Akahira Toshimasa, head of Mitsuhama's Thaumaturgical Research Division and hires the runners to investigate the Bone Church of Sedlec. There's reference to MTRD being responsible for the shedim outbreak in Prague the year prior and the Shinto religion judging Toshimasa as an "evil sorcerer." This sounds like the basis for him to be master shedim, no? Or...
b) Takes over the body of a Doanescu Rom talislegger who hires the runner to retrieve bones from the church. The runners will be hired to acquire bones from the church with the idea that they'll be paid well for their black market value (fits with the information given in the section on the Josefov district area).
Either way, I'm thinking that since master shedim are said to have a twisted sort of interest in the physical world and Threats 2 also eludes to the fact that they may have a desire to amass standard shedim under their control, this would be a plausible type of situation.
If I go this route, I'm considering having the Order of St. Sylvester send a father/mage to intercept the information about the run and arrange a meet with the runners at The Drum (which sounds like the local night hot spot in Prague). Before he can give them information regarding what the Bone Church actually does, he will be murdered... either by Mitsuhama goons or by the master shedim himself. If the runners investigate the murder, they'll be able to eventually gain the information the father was going to give them.
This brings up my next question. There's not a lot written about Kutna Hora Ossuary, but enough to whet my appetite. Is whatever is inside that is "collecting" shedim speculation only, or is there some other canon snippet somewhere that explains this a bit more? If not, anyone care to take some stabs or toss some ideas my way? I've gone from thinking that a master shedim is inside to a new type of spirit, possibly one of bone? Ideas?
Also, anyone care to throw in their 2

as to what the barrier mechanics are for the church? SOE implies that the shedim could possibly be released by ignorant runners. I'm curious as to all of your thoughts on how this might be possible.
Either way this run goes (whether by talislegging or by MTRD's interest), I'm planning on Jehuda ben Belazel showing up via the eyes and ears network of gypsies in the area with a team of golems to stop anyone foolish enough to go through with the plan. I'm hoping there's enough warning lights by that point in the story to get the runners to not go through with the run and instead figure out a way to remove the master shedim from his position of power. Phew! Thoughts...