2. The odd setup you have can be easily fixed. I suggest you move (copy) the bootmgr to C. Then you can forget about the system partition and you only have to image C.
http://www.sevenforums.com/tutorials/209885-bootmgr-move-c-easybcd.html
I have to disagree. Partition C: as shown in the OPs screenshot is the 2nd partition on the 2nd HDD (Disk 1). This is not a good place to put your OS.
It will end up being called C: but should be in the location E: on Disk 0 of your screenshot.
On a spinning HDD the OS and installed programs should be on the outer tracks of the HDD for speed.
Also I'm not sure that the EasyBCD solution will retain the F8 safe mode boot function but restoring the system reserved using x3 system repairs should retain the F8 function.
It is assumed that the OP still has the image to restore from. As I've said before don't have the 2 HDDs connected when doing this.
WHS your suggestion may be simpler and should work but I don't think it is ideal. Of course up to the OP.