For PDF transcription, the only software I've had any sort of satisfying results is with Visiv SharpEye. However, the only way I could transcribe sheets were page by page, and I needed to convert each page of the PDF to individual TIFF images. The results are quick, and when it works it works wonderfully. Editing the results is very easy, and then you can export to MusicXML.
However, I do not recommend this process as it may seem easier, there are so many things that do go wrong, especially when it doesn't interpret the number of voices in a staff correctly, and you need to do so much cleaning up to the piece after you've finally imported it into your music notation software. When transcribing music from PDF, I have always been most satisfied with inputting it note by note myself. I'm sorry, but computer software hasn't really caught up with this concept, I don't think. If you want something done, you got to do it yourself.