Mate, I know this sounds really gay but I am so happy I could kiss you!!!

You are 100% correct, however in my case the Virus had obviously been deleted but the antivirus had not restored my shell info.

I would recommend everyone follows the steps provided however I only did the last one which was changing the the Shell script to "C:\windows\explorer.exe"

Once again! Thank you so much! Windows not only starts without me manually entering explorer but it does it way quicker too!