I find it pretty confusing that you specified you are transforming in XML or PDF. Do you mean HTML or PDF?
In case you are working with XML, which specific language are you using? Are your XML documents in one of the most common XML document types (DITA / DocBook)?
Could you try publishing one of the predefined samples from the oXygen sample project to HTML/PDF and see if the transformation takes as long as it takes for your own project?
Sometimes, not only the size of the project determines how long a transformation scenario would take to complete.
It could depend also on the number and complexity of other resource references (like XSL stylesheets, schema files, etc.).
If one/some of your files are trying to access resources hosted on an external server could also affect the transformation time, if there is a long response time or if the server can not be reached at all, so you should try disabling your internet / LAN connection for a short while, then retry running the same scenario and see if it takes the same time to complete. If the transformation fails when you run it without connectivity, then most probably you have external references that are not reachable, so you should send us the complete transformation log from the console in order to investigate further.
If you already obtained and saved a transformation log, it would be great if you could send it to our official support email address