you have the tranny, but its not the right one.
if the 3SGTE came from an MR2, you have the wrong transmission because the MR2 is mid-engined RWD setup. and if the 3SGTE came from a Celica ALL-TRAC, you ALSO have the wrong transmission because the ALL-TRAC is AWD.
Neither MR2 or Celica ALL-TRAC transmissions will work, in order to do a 3SGTE swap you need a FWD transmission from another S series motor. from either an older Celica FWD with a 3SGE (non-turbo) or from a Camry with a 5SFE motor. on top of that you will need to upgrade the clutch to something that will be able to hold the power that the 3SGTE will give you. On top of this you will need custom mounts for the transmission to fit into the AE92.
You should've researched this swap before you bought it because basically with the motor you have, providing that you did get a 3SGTE with an uncut wiring harness and ECU, you're only half way there.