I am not certain the partition offset is involved, and I think the could only change it by doing a reinstall.... There may be some third party software you could try, but probably not worth the effort. I will need to do some more research, but I was thinking SSDs were more critical in their configuration. Since Windows would not install that way, I suppose you placed the install on the drive using some software?
I understand Windows 8 has a problem with having the User's files in a different location, but I have no definite info. I don't use any special procedures on my SSD since I feel it is large enough, so there is no reason to do so.
I have a motherboard similar to yours, a ASUS P8Z77-v Pro. The driver for the Intel Management Engine is on the ASUS site in the Chipset section.
Along that same line, you show two ASMedia XHCI USB 3.0 controllers on your system. I used to show XHCI in Windows 7, but Windows 8 has always shown as ASMedia USB eXtensible Host Controller, and I see no driver downloads for those controllers. If you were to have the External drive in one of those ports, you might try changing it to the Intel USB 3.0 port for testing.