Ok I hope it helps - when you say 'Games folder' just make sure that's not in program files/games! if it is change it to C:\Games\etc will be good

Also I would say keep copies of the Mods elsewhere and just move duplicates into your SH4\Mods\ folder when you want them installed it's just safer for keeping the original files intact if you have to re-install later.
P.S. yeah fingers crossed for a nice strong wind to blow all that ash out of the way! Happy hunting.