I wish HD would sync to PC, ESword LT, or somewhere but it doesn't.
What makes you say that? If you backup your iPAD to your computer, HD gets backed up along w/it (including your customizations - highlights, notes, etc.)
Note: based on the fact that customizations are saved when backing up the iPAD to a PC (iTunes backup), it stands to reason that a cloud backup would include the customizations (in fact I believe that is all that gets backed up - the app is already "in the cloud").
If you want to verify: backup to PC, followed by a backup to iCLOUD, then wipe the device & restore (from iCLOUD). If the cloud restore fails to include your customizations, you'll have a backup on your PC that will.
Shalom