To get rectangular nodes, you need to change type "box" to type "rectangle". Moreover, yEd does not use the name tag, but a label tag. Use a text editor to search for all type "box" and name ocurrances in your GML file and replace them with type "rectangle" and label respectively.
To have your labels appear in the north west corner of your nodes, you need to add a LabelGraphics section to each node section in your GML:
For additional properties, create a sample diagram with one node styled according to your requirements and save it as GML file, then inspect the created GML file. Note, though, GML is a legacy format that does not support all the available visual features. E.g. yEd's default label are not supported. For node labels, you should use the Internal model, for edge labels the model 6 Pos instead.