Here's a thing the Heritrix does that HTTrack doesn't seem
to do:  It will attempt to download all the parts that make
up a page, considering them all part of the same object. 
All frame contents, pictures, embedded objects etc that are
required to redisplay the page the way it was should be
downloadable as one.  You have only the 'near' option, which
doesn't cover frames at all.  That kind of 'closed' page
download could be very practical when trying to download a
limited part of a website.  Would it be hard to do?  Can
plugins get the info required to pick the right pages (i.e.
context of links)?
-Lars

P.S. Congrats on getting the pages well back up again.