You could spend years trying to get this right, it's just as painful as trying to use a Jira database with SQL. You will need to work out every relationship and cross reference it all in a flat file that does not have any form of relationship handling mechanism (so learning XSLT and XML parsing would be your first step, followed by understanding all the code for every plugin in Jira)
The best approach depends on what you're really trying to do here.
If the data-centre system is a new empty system, then your best option is to delete the projects you don't want from the old system (or a temporary copy of it) and then import an export of the resultant system. You could also just import everything and delete later.
If this is actually a merge with the DC system, then your best option is to import one project at a time from the export, after manually creating the container project. I'd strongly recommend a look at apps like Project Configurator and Configuration manager, as they can help you copy projects from one Jira to another, solving all the conflicts and taking the configuration as well. (I work for one of the vendors of those two, but I'll still say you you check them all to see which may work best for you)
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