Sorry I haven't replied sooner, some personal stuff has nearly destroyed me, so I haven't felt like coming around much at all these days. Anyways...yeah I have WinHTTrack sitting around too, but haven't used it much. As far as I know, it's really only good for cloning a site? I think it's near impossible to auto-backup that Wayback Machine archive with existing tools, since you can't really auto-follow each link with them. Whenever I do it these days, I just save each page in whatever browser I'm using. It's painstaking and time consuming. Maybe others know a better way.

As far as merging those archives, I think you would have to go through the HTML and re-connect all of the links that are now different. Added bonus would be to delete all of the links that weren't archived. One quite old batch tool that I like using for changing links is SearchAndReplace V2.5.1.0. If someone knows a better one, I'm all ears.