I replaced my Hard drive and restored everything using my Time Machine BackUp however when I start up Paralles it states there is no Windows Operating System. Time Machine restored the Windows Application Folder so everything appears to be there so what are the steps I should take to get up and operating again?
Windows application folder in Finder is just a set of links to Virtual Machine. It cannot indicate if the VM has been restored in a proper way. You need to contact Parallels technical support in order to investigate the issue. You can use chat or submit suport ticket - choose the way which is more convenient for you.