I had this when first syncing contacts to Google via Nuevasync and MfE.

Your only salvation is your backup (what do you mean you didn't make a backup? ;>)

Delete your exchange settings. Upload all your optimised and checked contacts to your exchange client (Google, in my case)
Make another backup of your contacts then delete all contacts on the device. Re-establish your snc settings.

Your N900 should now download all contacts on the first sync. Subsequent syncs will tend to produce duplicates; these may be whole duplicates or duplicate fields within some contacts.

Google has an engine to remove duplicates and allows you to edit contacts to ensure they have the same format.

Ongoing syncs will produce sporadic duplicates and you'll need to check periodically, but sooner or later you should see your contacts stabilise.

Tips:

Keep contacts simple. Multiple fields on the same contact seem to increase the chance of duplicates; consider splitting some details off to make a new contact with a similar name: e.g. 'John - Work' and 'John - Home'

Initially, make changes at the client end (if possible)

Only sync one device to one client; if you run multiple devices sync one initially, then add the second. before you add a secon device, make sure it has no contacts beforehand.

Keep backups - and good luck, as that seems to be part of the process!