That's an impressive amount of work. I bet your fingers were getting tired after all that tapping.
I have to say you have a lot more patience than I do.
To answer your previous question the manual isn't available for download. Allowing Active X content to run from your CD drive and from the hard drive (first 2 items in Internet Explorer Optins/Security is not a bad thing and many programs now use those types of scripts. This does not allow them to run from the internet as that is a separate control. As far as McAfee screaming about it you may need to change a setting in there too to allow this. For the manual it allows you to click on an item in the table of contents and go directly to theat subject/section. I don't think the earlier manuals have this feature so this may be why you are only seeing the message now.
To go back to the slow duplicate, I did forget to mention, that in previous version including 4.006 you had an option in the Default Drives tool to choose Good, Better, and Best settings for the drives. This defined how much error correction and I think the write speed. You no longer have that option and all settings are for the best quality in both cases. This I am sure is contributing to the slowdown. If I remember right from the beta testing the Duplication was taking roughly 10-15 minutes for the whole process. And this was no slower than using Roxio to do the same thing.