Hi Joseph,
There are a couple problems I saw with your project file. You need to either add signal delay to every bidirectional component manually or check the Initial Delay box in Layout Parameters->Signals. For more information on how we model bidirectional devices please review our tutorial at:
Lesson 5: Bidirectional Simulation — Working with Multiple Iterations
1. The power meter should calculate the average power over all wavelengths.
2. Yes, it should include the modulated part in the signal.
Finally, for a bit rate of 10 Gbps simulating a time window of 1 second will require a lot of memory. For a samples per bit value of 64, the total number of samples required is ~640e9, and so using a 8 byte double as an estimate the total memory required is roughly 5120 GB’s!