I had the same problem upgrading a Mac Pro from Windows 7 to Windows 10.
The Windows 10 Upgrade Assistant got to 90% within 30 minutes, then took a few hours to get to 99%. Everything else on the computer worked but the status showed 99%. I waited and waited. Eventually, while I was sleeping, Windows 10 got to 100% and installed. I estimate it spent about 14 hours at 99%.