Thanks for the replies, everyone...but unfortunately it definitely is the transmission.
Trading it in is not an option with it's clicking condition. The JDM transmissions all have the an oil cooler mounted high on the passenger side of the transmission and also they have an electrical box on the lower driver side of it...both of these applications don't apply to my car, as told by the Subaru tech and is visually correct when viewing my cars original transmission.
This really stinks, as the secondary market for these transmissions are very high and a brand new one installed is $7,300 by Subaru. The JDM's are actually better transmissions and less expensive, as told to me by a Subaru tech, as their engines are also, but out of luck when it comes to their transmissions for a '13 Legacy.