I don't know if it will entirely solve your problem but I may suggest a few steps regarding the USB boot, from what I learned setting up a dual boot (bootcamp) with no superdrive (two disks, like you) :
You need to make the BootCamp Assistant think you're a Mac with rights to boot on a USB drive. To do that :
Go to Applications/Utilities Right click on Boot Camp Assistant and select "Show Package Contents". Open the Contents folder
Open Info.plist with your favorite editor. If you don’t have permission to do that, copy the file on your desktop. Once you’ve made the changes, copy back this file in the folder.
Click on the top left Apple menu of your Mac, go to About this Mac. In the opened window, click More Info. In Hardware, find Model Identifier (Mine is MacBookPro8,2) and find Boot Rom Version (Mine is MBP81.0047.B27)
In the previously opened Info.plist, copy/paste the previous info on top of the list in the correct field: In DARequiredROMVersions, add a string that matches your Boot ROM Version. For instance, mine was:
<key>DARequiredROMVersions</key> <array> <string>MBP81.0047.B27</string> <string>IM41.0055.B08</string> ...Go to USBBootSupportedModels, and add a string that matches your model. It’s a bit tricky here, but you need to find the right model. For instance, I have a MacBookPro8,2, so I had to write: MBP81. If you have a MacBook Air3,2, you would have: MBA31 etc… You can try several times if it doesn’t work. Here is what I added:
<key>USBBootSupportedModels</key> <array> <string>MBP81</string> <string>IM130</string> ...Once the info.plist has been saved (and copied where it was before), double click on Boot Camp Assistant, the greyed check box « Create a booting USB drive » shouldn’t be anymore. Then, create your BootCamp partition as usual.
What can happen next is that the Mac can reboot, cannot boot on the USB drive, and cannot find how to boot on the Mac partition neither. Don’t panic, just press the hard button and reboot it again, plugging out your USB drive. Tip : where we finish installing Boot Camp partition and rebooting, if you keep getting the "No boot partition found blank screen", just reboot again and hold down the « Alt/option » key so you can select your main MAC OS and reboot that way.
It worked for me, no reason it would not for you.
Here is my source (for the whole tutorial but I guess you do not need the full version) : http://huguesval.com/blog/2012/02/installing-windows-7-on-a-mac-without-superdrive-with-virtualbox/