Help my with my Graduate Project's Idea to make it real by using FPGA

I agree that the USB protocol packets need a quick acknowledge, and it's not possible to directly send low level USB signals on 100m of fiber. You will need to decode the USB protocol on the first board and send data as a custom serial prototol on the optical fiber. On the other side you will need to decode your custom serial protocol and translate it back as USB host commands. I think this will be a lot of work, and there aren't a lot of USB cores available, at least for altera FPGAs.