(The following comment turned out to be the solution:)
Using your highlighter.java
class (provided on your google drive in a comment) together with the current PDF Clown trunk version as jar, the PDF was processed without incident, especially without NullPointerException
(the highlights partially were not at the right position, though).
After looking at your shared google drive contents, though, I assumed you did not use a PDF Clown jar but instead merely compiled the classes from the distribution source folder and used them.
The PDF Clown jar files contain additional ressources, though, which your setup consequentially did not include. Thus:
Your highlighter.java
has to be used with pdfclown.jar in the classpath.