The Dead really put a kebash on the availability of soundboards. The ones from Archive.org were first to go, but many could still be found at www.GDlive.org. That too is now down.
Many shows still available here: http://www.mininova.org/search/?search=grateful+dead
As for burning, do you have the most recent version of iTunes? I think that handles gaps better.
If not, try EAC http://www.exactaudiocopy.de/