Hi,
Yes, it should be possible to do that. Please send a screenshot of your filter setup to
support at yummysoftware dot com
I'll take a look and see what's going on.
To answer your questions:
There is no cached information kept about the files and folders that have been synched. Unfortunately, the only really reliable way to ensure only the required items get transferred is to not make any assumptions about the directory structure, both remote and local. Several hours does sound like a long time, but there are a lot of factors such as actual number of files, server speed, your line speed, even your Mac's speed, etc. that need to be taken into account.
There is currently no way to set a pause and resume time in a schedule. If you want to avoid overlapping synchs, I suggest limiting the number of simultaneous connections to one, which will force a scheduled item to wait if another has not yet completed. You can set this restriction in the Advanced Settings tab of the editor for your Bookmark.
For email notification of any event, including synchs and errors, install Growl (
http://www.growl.info) and use the Email Me notification.
There is already a Synch Completion report displayed at the end of synchronization. It would be reasonable to add other statistics to it

There are no options to name schedules at the moment.
For the delete orphans problem, Yummy doesn't make any assumptions with your filters. You need to exclude both the local and remote items, otherwise it will appear to the synch engine that there are items which are orphaned.
Thanks
