i WOULD MAKE SURE THE GAS PEDAL IS MORE TO THE RIGHT.
Most autopedals the brakes pedals are more left and then when a manual pedals install they move closer to the gaspedal and it will be a issue in a panic stop. Believe me.
as for the maniold port i seen alot of l16manifolds with a port attachement on there so it should be EZ to find. Even thought its the forth runner its all hooked up the the manifold pressure on all the cylinders unlike soem sidedraft type manifold were its actuall on the 4th runner and make a pulsating issue as it only on the 4th cylinder.
hopefully you have the correct T/O bearing & cllor for the clutch as its based on the clutch prssureplate/flywheel and not the trans. set up. example 225mm L20 bolt use a 620 truck set up. If a 200mm nflywheel L20 6bolt use a 510 or Roadster setup.
for the stick shifter side plastic bushings One can use the Cryslers door hinge bushing for the trans shifter. I find soem plastic just dont last long and disinigrate. the HELP brand at O Rileys had a assorment of sizes in a pakage and I inserted then using a vice. the pin didnt go in but open them up with a drill bit till trans pin would fit.