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Here's my suggestion (assuming it's your right hand you have use of).
Get a Razer Naga: http://store.razerzone.com/store/razerusa/en_US/pd/productID.169418900/parentCategoryID.35208800/categoryId.37466100
I play with the hotkeys in grid mode (command button windows grid matches the QWERT, ASDFG and ZXCVB lines on the keyboard). You could do something very similar with the Naga, where the top line of buttons is 3, 6, 9, 12. You will be missing the 5th column of buttons from the grid, but the mouse does have 3 more buttons elsewhere (wheel click and the two on the left side of the main left button). The mapping for those is less natural, but it would work well enough once you'd gotten used to it.
Then get two USB devices to serve as your control and shift buttons. These would be easy to hit with your elbow, or even feet (use them as pedals). Here is a guide to making one out of the Staples easy button, but they are avaliable commercially also: http://www.instructables.com/id/USB-Easy-Button/
For the USB buttons, it would be extremely easy to make a quick AHK (http://www.autohotkey.com/) script to get them to function as control and shift. I don't have a Naga, but the Razer software looks fairly complete and would do the job there. If not, it would still be quite simple to write it yourself with AHK.
With that setup you'll have access to almost all of the hotkeys a regular two-handed player does. The ones you're missing (such as the dedicated hotkey for warp gates) shouldn't be too much of an issue.