LTSpice, can I have separate plot panes?
Unfortunately, that's not possible. But you can run multiple instances of LTspice and you can load the .raw file and select whatever traces you have. The downside is that after each run, the .raw file will need reloading for each of the external instances of LTspice.
One thing that could help is to save the plot settings (make the waveform window active, click save). Then, when loading the .raw file externally, the waveform window will show the saved traces.
Or you could use the .step command to get all the desired traces inside one plot, in the same window.