You can read a long PDF faster by splitting it into shorter PDFs, and tackling one chapter at a time.
iAnnotate on the iPad is an excellent app for annotating and marking up PDF files. A companion app, Aji PDF Service for Mac, provides an elegant way to serve PDF files from your Mac to iAnnotate on iPad over a wifi network.
Use PDFExplode to split a long PDF into several short PDFs, say one PDF for each chapter. Then, markup one chapter at a time in iAnnotate and sync back with Aji PDF Service on the Mac.