Even though PDFBox is written in Java, there is also a .NET version that is available. It utilizes IKVM to create a fully functioning PDF library for the .NET framework. The released version contains a bin directory with all of the required DLL files. For the command line applications that are available in the Java version a native windows executable is also included. This page contains information that is specific to using the .NET version of PDFBox.
PDFBox no longer requires log4j! Older versions used to require you to configure log4j before using it in .NET
The way that IKVM works is that DLLs are only compatible when used with the dependent DLLs that are used to build them. For example, in order to build the PDFBox DLL, a lucene DLL needs to be built, then the PDFBox DLL. The PDFBox DLL now depends on that *exact* lucene DLL. This means that if you build your own version of the lucene DLL then you also need to rebuild the PDFBox DLL. Your best bet is to use the lucene/pdfbox that is shipped with PDFBox.