I believe that the Wired app lets you re-downloaded issues already paid for, so my suggestion would be to delete the Wired app from your iPad and try to back-up you iPad again, if it continues to be slow then you might have another issue.
If the problem goes away then you can say for sure that it was the Wired app. At this point just re-download a new copy of the Wired app and its Issues one at a time, back-up in between and see if the problem continues.