Stuck in the Chancel

I've got the orb pieces, put them in the pedestal (with the tar), but I don't know what to do with the bone, the jar with the string attached to it, or how to create "Weyer's Tonic".

You have to go to the Laboratory in order to create Weyer's Tonic.
In order to get access to it, you have to have obtained the six orbs (like you have), after which you'll have to get captured in the Chancel. Only then,

upon your subsequent escape from the Cells and flight from the Shadow, the quakes will cause parts of the castle to collapse, making the Laboratory accessible.

Once you're in the laboratory, you'll find all the equipment you need to create the tonic using the following steps:

• boil the blood on the burner to extract the Vitae;
• place the jar under the vice,
• put the poison gland in the vice and crank it until it is squeezed into the jar [in no particular order].
• Finally, put the jar under the contraption on the center table, and place the Tampter-covered bone inside of the contraption. This will steam the > bone and put the Tampter in the mixture.

The potion is now complete and ready to be used.

^source