Does anyone have any good personal systems for ploughing through scientific reading?
Without a good system in place I'm feeling daunted and a bit paralysed.

Read for a purpose, such as writing a literature review. Then it's more focused. Keep PDFs highlighted with relevant sections in something like Mendeley, which is also good as a searchable database later on.

I second that. Also, search this forum for existing threads on this topic or similar. I know it has come up before and people have given really detailed and helpful responses.