I finally got my 2.4 swapped in and now I'm putting the car back together but can't find information about the tcase install, specifically where I need to put silicone to prevent it from leaking and where to get new seals/oring. Any help is appreciated

 

There are dozens of writeups. And you shouldn't need to put silicone anywhere to prevent leaking. If your seals are bad, they're bad. Silicone isn't going to help.

http://www.evomoto.com/tech_info.php?tech_id=27

 

One of the write ups I read stated to put silicone on a protrusion, and I don't see the protrusion.

 

The only protrusion you need to pay attention to is the 4th gear relief on the 6-speed. Most people decide to use this as a leverage point to get the thing out of the car, and that's a very bad idea.

You're welcome to get the service manual downloaded (free) from here: http://www.evoscan.com/vehicle-manuals

But you don't put silicone on anything.