The folder structure you set up in Synergy - can this have files included? So when you create a new project it gets the structure in SharePoint along with the files? we have .OFT files in there, some PDFs also word docs, also .xksx (we have lots of files in our default folder structure template it seems)
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We can't pre-fill Synergy Folders with files at this stage although, that's a good idea

In SharePoint, we have different document libraries for every 1000 projects. This is because the number of files we have can be very large. Is this handled gracefully in Synergy, or will we need to reconfigure it every 1000 projects?
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At this stage, it works with one Library and makes sub-folders for the projects. We would be happy to get some more details from you and look into this further.,

Can project documents be locked to nominated Project Managers only (eg sensitive projects)?

The folder locking that is managed by Synergy based on 'role'. It is possible in SharePoint to add further security, however, this is not carried through to the 'saved revisions' in Synergy.

What sort of reporting (in Synergy) is available for transmitted documents? I'm talking about the existing download to XLS type reports?
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There are currently some nifty on-screen reports that show who has received files. (click on the 'shared with link')

Can you get a drawing register for all final drawings?
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Yes, the Synergy Document Register shows the current revisions of all documents. Previous revisions are also stored and can be accessed if required.

Is synergy looking at a signing feature for docs?
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No not at this stage.

Do the files stored in SharePoint count towards the 5Gig storage limit in Total Synergy? This limited storage has stopped me from using Total Synergy for file management as not enough space.
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No, only files shared to Synergy count towards the 5G allocation. The shared files tend to be PDFs, which are generally quite small. Note also, you can purchase more storage if you need it.