I would first see if you can fix the problem using a restore point or other method. If you run the restore set from the PC manufacturer it just resets everything to "out of the box" condition. A better solution in the future is to have external USB drive to save system images. There are free programs that let you make a backup image such as Macrium Reflect. But you can find more at:http://www.thefreecountry.com/
Also it is a good idea to use many "portable" applications. I have many small programs that only use .ini files for settings, in folders underneath C:\Utils.
Even if I put on a new Windows using a Custom Install all I have to do is make new shortcuts to use them.
Unfortunately since the registry is so complex there's no easy way to save whole installed programs other
than just making an image of the entire partition.
I would try to find a specific fix to the download issue because if you do the system reset you'll have to reinstall everything all over again.