Direct purchase using PayPal ($40 only per license, both tools included)!
This tool allows you to select whether to convert links, fields or bookmarks. It looks like this:
Update: Now available are demo versions of both tools, which will process up to 3 files, 3 pages per file and 3 links per page. You can download them from here.
These tools run independently of Acrobat and can process an entire folder of PDF files (and all sub-folders) in a single go.
If you have any questions regarding this tool, you can contact me directly.