Read cerefully, please = ammended.
Mate, I've got multiboot system as well - 3 Windowses and 5 linuxes, 2 bootmenus - everything on 3 drives (one SSD and HDD RAID-0 setup) and unfortunately Windows 7 bootmenu uses EBR and rest use MBR, so it's some kind of pain, especially once I disable one drive with no proper preparation each of them. Windows 7 is soo special

and names boot partition with "C" always, so you probably know that - depending on boot, D drive points not always to the same physical drive, but other than boot one.
I think your problem is here. If I were you, I wouldn't plug in second drive until everything is installed properly @ both drives, but this must be done twice - separately, for each drive. Once it's done - I'd plug them both, boot* from C and use
EasyBCD software to check if everything is fine with bootmenu* and
drive assignments which I think are clue of your issue - not drivers**, not BIOS settings etc (and to re-create bootmenu files, if needed). After that, I'd boot* from D and use
EasyBCD again to do the same thing. After that I'd be sure that disabling/taking out the second drive is fine for booting the whole machine, and not some "bootmanager file is missing" message. Blame me, if you still have USB issues with system built this way.
* boot, bootmenu - I mean Windows 7 bootmenu, so you must have 2 entires there. Booting via BIOS bootselector might cause issues as described.
** do not focus on drivers at all, mate. If it were drivers issue, you woudn't have working system booted from C drive. Please notice issues start with D drive = so it's all about drive assignments for 99%, as I wrote. Oh, and BTW, next time you might try this installing order: -Windows, 2-drivers (previously downloaded from website = newest), 3-Service Pack, 4-Updates.