Since there's no real windows installation, practically speaking, in your situation, I would remove all partitions. Then, using your drive manufacturer's disk utilities, do a surface scan of the drive to mark bad sectors. And yes, that will take time. Make sure your SMART monitoring is turned on, too (in the bios), as this will detect failing drives often.
Once all of this is completed, assuming the drive passes testing, go ahead and format/repartition.
By the way, the Ultimate Boot CD (FREE) has many disk utilities you can use. You can boot up with it and choose one of the disk utilities from the menu. Get it here and burn it as a bootable ISO:
Ultimate Boot CD Download