Update: 1/3/2017
So my service manager told me last week that Toyota suggests they disassemble the motor so that we can find the source of the problems. This is the current state of my engine:
He also mentioned that they found metal shavings in the oil but were not aware of the source of the shavings in his text to me this morning.
I asked for an update in the afternoon and got this response that I'm not sure how to take currently...
"We found a very small oil port with a restriction that appeared to be the sealant that is used between the block. Toyota is sending someone tomorrow to inspect the engine now that it is disassembled."