1. How to include all fonts
If you are using Adobe Acrobat Pro X and above:
Go to Tools>Preflight
Type in Embed in the keyword, you will get Embed fonts under PDF fixups, click Analyse and fix to fix it.
2. How to remove bookmarks
- Remove the \hyperref pacakge in latex
- Print the PDF into another PDF will do.
To check whether all fonts are really embedded, See how to check all fonts are embedded using adobe reader.