1. I found many Mega downloads had that problem on FF. When I used Chrome just for the downloads the problem diminished.
2. On either FF or Chrome one time ... can't recall which one or if both ... I discovered a drop down window I hadn't noticed at the top of the screen asking if I approved multi-file downlods. It was not eye-catching and easy to miss. If I didn't say yes -- a one-time answer -- stuff got stuck at 96% to 99%.
3. When I have folders with large files I just drill down into the folder and download the files rather than a whole folder of them. There hasn't been anything I couldn't download doing this, it's just a time-consuming work-around and you have to organize the downloaded stuff into the appropriate folders. Minor price to pay.
Hope this helps, rather than having to wait for some kind soul to create another mirror.