These instructions are very specific to Apple Macintosh users. Once I have a similar options for windows users (or one of you windows people provides steps) I will create a full page just for this topic.I added a module that I had be testing that enables "print all" for a topic (thread). It "should' address the need for folks to make their own archive.
The issues with formatting though are really safari problems. WebKit (the core of safari) dictates the page-brakes and such. The solution is to "not use" safari to print. I found the best method requires the new module (and you will need a lot of paper is you actually print it). I'm a Mac guy so I'll provide the directions I think you need.
1. go to your topic (thread)
2. click the wrench drop down and select print all
3. once the page is fully loaded, cmd-s (save as from the file menu) and save to disk.
4. in finder locate your file (it will end with "webarchive")
5. control-click the icon to get the pop-up menu for finder options
6. select "open with" and then "text edit".
At this point you have the thread open in a tool that can properly paginate. At this point I recommend using the file->save as to pick a format like RTF that can be used in many different tools. You can also use text edit to export to PDF in a usable format.
Let me know if there are any questions.