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Can I use the last available port AI3 for two single ended connections (with different grounds)?
I am confused by your "different grounds" comment. Each of the single ended signals have a different ground? Or just different from the differential signals? In the end, all of your signals must be referenced to the same ground. This can often be done with a simple 1MOhm resistor between the grounds or direct tying of them together. So you might want to give this article a good read: Field Wiring and Noise Considerations for Analog Signals.
Now to your actual question: The connection mode is set on a channel-by-channel basis. So you can use AI0, AI1, and AI2 at differential (AI8, AI9, and AI10 being the negative side) and AI3 and AI11 as Single Ended.
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