Sorry to hear about your troubles. For $400.00 you could practically get a new hard drive!
Heck for $400 you could get an entirely new computer!
Computers can be a pain to deal with. They are just not designed for someone to fix easily. I had a simular problem with the power supply frying the motherboard. Fortunately, the hard drive was ok. I pretty much built a new computer wth a new hard drive in it. Once I got everything including the usb to work, I copied my data back to the new hard drive from the old hard drive. I kept the old hard drive in as backup.
I bet all they did was install the new motherboard with the old hard drive and saw that it booted correctly but didn't try any devices. The correct way to install a new motherboard is to format the drive, reinstall the OS and programs. That is the only way you make make sure windows doesn't get confused by the new motherboard. I think windows is trying to use the old motherboard's usb drivers and won't install the new ones because it thinks the old ones are newer and correct versions.