Jim that was not an easy long paragraph to follow along. Can you create a video and show what you're talking about.
I highly doubt there will be a separate waveform for each model view. You can use the Views feature to show/hide certain models in your sequence.
As far as creating custom effects (Presets they're called in NC), you can import effects from LOR which is just importing the LOR LMS,LAS,SUP file and those effects are displayed as an equivalent NC effect. You can then save those effects to your NC Presets.
If you don't have a WHM in any sequence yet, DO NOT USE THE WHOLE HOUSE MODEL Feature. It is there for backwards compatibility. Use Model groups instead. I repeat DO NOT USE THE WHM feature.
Your sequence should have timing marks from start to end. There should be no blank space in the sequence because you'll having timing marks from start to end. What issue are you having? Put that in your video.