As long as your version does take place within established canon - even if it's an alternate or optional path - then it's totally usable. If the character can be female in the game, then you're free to play them as female.

I admit I'm not familiar with the Omni-tool myself, though from the description it sounds pretty powerful. It's cool if you want to have her integrate the device with the PCD, tho', as long as the tool itself isn't all-powerful? As in, it still couldn't be able to hack through what players consider unhackable entries (without permission, etc.), or create a limitless amount of grenades/items on its own, if that would be alright?