'low level formatting' hasn't been possible anywhere but the factory for decades now. What did you actually do? Checking what? The bad drive, or the new one? Only you'd know whether your data's any good. If your application can't tell you, then nobody knows. Application errors can't corrupt a filesystem, though. That takes a hardware or kernel fault. (Checking dmesg may be illuminating.)

And if you're getting data corruption on good disks, something in that server must be malfunctioning, therefore any backups you make using that server are suspect. The longer you keep toying with the original disk in the original machine, the more likely it gets that something worse will happen to your data. Does your system have lots of free memory? If yes, most of it's going to be used as disk cache. That makes pretty good odds that disk will be the first thing trashed by a bad spot in RAM, in a highly unpredictable way. Which PCI sata card? It's easy to get a lemon. That basically means doing it in Windows since Cygwin isn't an operating system. It might technically be possible in windows but there'd be lots of hoops do jump through and proprietary software nobody would know how to help you with.

centos or ubuntu should do. I wouldn't reccomend using Microsoft Windows to manage partitions for any system except Microsoft Windows. Again, what do you mean by "low level format"?

The form of backup I'm thinking of wouldn't need partitions on the destination disk at all. It'd just be a raw dump of data from one disk to another, sector by sector, which clones all partition layout in the process.

Um, dd_rescue first, then RMA You kind of need the drive to make a copy of it.

dd_rescue will also tell you whether you get read errors or not.