Sorry, but I haven’t got the time to give that enough thought for a proper answer.
However I definitely think that any obvious shortcomings would have to be removed and that includes javascript timeout warnings.
We’ve now reverted to this method, which works fine for this number of files, and doesn’t have any javascript warnings – http://www.vendorconnect.com.au/downloads/
Another benefit of this method is that people can bookmark a particular folder so they don’t need to start at the root folder each time.