It sounds like what you want to do is get a backup of everything, from the partition mapping, to the OS structure, to the data, that is currently on your hard drive. What I would do in this case is get Linux back up and running (ie, fix GRUB, which you should be able to do with either a re-install of Linux or with a bootCD and getting in there and reinstalling or refreshing GRUB) - and then, before doing anything else - grab a copy of CloneZilla
CloneZilla is a drive imaging tool, so it will create a high level image of your drive; it will basically be agnostic to what you have on the drive, and it just copies the drive itself, from first bit to the very last bit, to another drive. If you ever needed to restore, then you can do the reverse: copy the image back to the hard drive.
This is an imaging software, not a "backup" software, so you would still want to do incremental backups of important data. That way if you do have to re-image, you can re-image, and then "apply" your incremental backups back over your image to bring it back up to date.
But in terms of preserving your drive's structure to avoid any accidental erasures of partitions or bootloaders, I think CloneZilla is what you are looking for. I used it to image drives all the time back at my old sys admin job.