First, off: Welcome to MobileRead!
The PDF thing has been a known problem pretty much since the beginning. If you don't have access to recreate the PDF's in a size suitable for the reader, your options are pretty limited.
There are a number of threads in the Content subforum which discus various efforts to convert PDF's into more flexible formats (like RTF) that display better on the Reader. The results have varied, and I don't think anyone has a magic bullet yet.
For my own part, I just try to avoid PDF's for now.