Ah, I was going to ask for an example, to see if you also have a formating issue. That is, I believe HTML formats supscripts, superscripts and the like differently, causing a whole host of problems when put into Word. But it looks like (even though the gifs didn't come through on this end) that the authors are using gif's in place of characters. Which is a common work-around for the font-format problem.

So, what to do?

Have you considered composing your compilation in a web page editor? Pasting html into html might work better. You'll still need all those gif's in your own folder, and the img tags may have to be changed to reflect each gif's new location.

Editing in Adobe Acrobat might be an answer as well, but you'll still be a cut'n and a paste'n.

Me, I'd probably would do screen captures then cut out sections using photoshop.

Maybe better minds than mine have a suggestion for an easier approach.