Mac/Windows file migration (and some viral woes)

Hello all,

My woes started when a killer virus ate up my machine caused BSODs to come up on me when I booted up. My cousin tried to slave my hard drive to his computer to save the data but for some reason, he could not lift the protection off of the files (apparently I set my files to be encrypted/protected? Although I don't remember doing any such thing for all my files...) and thus couldn't rescue anything

I was curious to see what would happen if I slaved my hard drive to a mac. Luckily, the mac was able to move files from the hard drive, but could not write to my NTFS external hard drive to migrate to my new computer. I borrowed a friends Mac formatted drive to try and migrate the data.

I rescued all the files I wanted but now I am at a loss of what to do. The immediate thing I can think of is to use my 16 Gb usb stick to migrate the files a piece at a time to my new computer or external hard drive. However, I was wondering if the it is wise to do so given the lack of file integrity USB sticks sometimes suffer from. What should I do next? Are my fears about the USB unfounded?

Extra info:

Some time later, I realized my USB was infected with a "taquito.exe" that was contained in some folder whose name was some series of brackets, letters and numbers. I deleted it along with the desktop.ini file (which i suspected was also infected, as the viral file folder kept coming up). The file was only visible when I used a mac with the USB

However, what also could have been responsible for the recurring virus was a computer that I liked to work off of in the school computer lab. As the viral folder came up after plugging it into a mac some time after using that specific computer (which I had also used prior to the major crash)

My computer became infected after a couple hours of playing with this tool.
hxxp://goggles.sneakygcr.net/
Although I see nothing totally malicious, it's heavy use of java might have opened up my system to external systems.

(tl;dr version: Given the timing of events, the virus could have been caused by the online tool or the school computer. I'm not sure which.)

When my cousin opened up the permissions folder while examining my hard drive on his laptop, a user with the same name as the viral folder I found on my USB was listed.

Given this information, is it possible that I could just slave the drive again, perform a virus scan on the drive and be able to use it again?

Thank anyone who helps in advance and apologies for my long-winded post