Hey,
I think your approach sounds pretty good. To answer your question about the EntityRuler, once the annotations are in the dataset after ner.make-gold, it won't matter whether they were initially predicted by the model or the ruler --- they'll still be in there, and the model will learn from them.
To answer your second question, you can try either: usually I recommend training from a blank model, but in your case, since you're using an existing entity type, maybe resuming training will work for you --- give it a try and see.
Finally, I think @ines's answer here will explain the situation with the feed starting from the beginning: Duplicates in ner.manual