The simple fact is... that converting from PDF to MOBI is going to be a very "hands on" process requiring manual intervention and much tweaking to get satisfactory results. It can be painstaking at times. You're better off producing a PDF that is designed specifically to be read on the screen-size of your device and forego the conversion to MOBI entirely.
The main reason for this is that PDF is a much better final destination for a document than it is an intermediate step to something else. The conversion to PDF should mainly be considered a one-way street.
If you care at all about the formatting of your ebooks... the conversion of 100 PDFs to quality MOBIs is going to be quite a daunting task.