To speed up Foxit PDF IFilter, you can choose not to index annotations, bookmarks or file attachments by disabling the options via the registry as you want.
1) Locate the following registry subkey:
HKEY_LOCAL_MACHINESOFTWAREFoxit SoftwareFoxit PDF IFilter
2) Disable the option(s) by setting the corresponding value(s) to 0.
For more details, please refer to page 16 of user manual.