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I know the solution using which you can indicate category name in the file and if you do not have such a category, it will be created on the fly right in the process of import. It is possible to to using the application called Store Manager for Magento. It has flexible system of data input and the modifications can be done right in the process of import.
Also at the moment we are working on the improvement of import procedure and further it will be possible to add huge amounts of products during one import procedure, so there will be no need to separate the file into portions.
In case you are interested, you can download the application here -
It is free 2-week version, so you can try it out.
In case you require any assistance, please, let me know.