Pull the bowl, you will need to cut the sealant between the bowl and the TA.
Also, you might want to remove the TA.
Do you have a rigid framed seal or a soft one?
Do not use silicone on the gasket, use High Tack or Hylomar. Use 100% silicone for the TA and the Bowl area.
Also, glue the seal to the bowl with something like Permatex number two or Yamabond.
Be very careful putting it back together.
Good luck