Getting PDF from Quirk is relatively straightforward provided you have Adobe Acrobat Distiller. Acrobat Reader is no good - you need the *full* Acrobat app.
Simply distill your Quirk doc to PDF. You may need to fiddle with Distiller's settings to get the results you want although version 4.0 does include some pre-set configurations (called settings files) specifically designed to optimize PDF's for the web.
Getting HTML out of Quirk is *not* easy. One route is to buy "Avenue Quirk" The downside is that it costs an arm and a leg.
Option 2 - use a Quirk xtension like "Beyond Press" from Extensis (www.extensis.com). It's about $300.00 and does a reasonably good job of converting the elements of the document into HTML and DHTML.
Quirk's own FREE extension "Quark HTML Text Export" (www.quark.com). This is decidely limited insofar as retaining the content of the original document is concerned.
Option 3 (which I use) is to re-create it all over again by hand. Tedious, but it ensures it's correct!
Other than that I suggest you lurk on "comp.publish.prepress" which is the only place on Usenet where you are going to find professionals discussing Quirk outside of Quark's own forums.
Del Tree (veteran comp.publish.prepresser)