I've been using
GetFLV. Yes, I did try to repair the standard HD vids, but to no avail. The only thing I've been able to do so far is as I've already described, which eliminates 90% of the stuttering but leaves the audio to a tedious fix! Luckily, not all of the vids I want are in HD, with most being Full HD, so I'm lucky and the Full HD's don't have any problems.