Hi Jake,
1) I was trying to find the source of error and the LiNb gives a more linear response, you can keep it the same if you want.
2) The BER Analyzer can calculate the BER from the eye diagram whereas the BER Test Set has to count errors. If your expected BER is 1e-7 you need an extremely long bit sequence to simulate, so that the system will create one error. The PPM is like a normal bit sequence, so the eye diagram will be similar to a OOK modulation format.
3-4) The reason I adjust the global bit rate is that a lot of components use the bit rate as part of their calculation (Filters etc.), and since after the PPM encoder the signal is basically a bit sequence with a higher bit rate I chose that as my global parameter. And yes you are correct about the bit rates.
However, you could definitely make this project anyway you would like and there is more than one way to simulate it. You could even still use the BER Test Set and count errors of extremely long sequences if you desire, although this would take long simulation times and you would need to make sure you bit sequence is large enough. The projects I have made and demonstrated are examples of how I might simulate this design, but depending on exactly what you want to investigate there might be a better or more efficient way.
Regards