Long story, but not happening.
I went through this EXACT misery in 2009 (I bought the very first Nissan Cube delivered in AZ) and wasted 3 years trying to convert to a manual (should have bought the 6mt in the first place).
The wiring alone is a nightmare. You'll need an entire harness and ECU from the donor vehicle (it's a CAN-BUS system, so unless you're well-versed in those, skip it). It ties into the HVAC, gauges and audio, as well as the airbag computer, so you'll also need all those bits.
After ALL that, and finally getting the trans to play nice with the ECU, the axles for the manual are different than the CVT model - AND the uprights (front suspension) are unique to manual or automatic. So, you'll need the front suspension. See where this is headed?
BTW, I'm no amateur, but lest anyone think this was a lack-of-skill issue, the GTR-cert tech from our local dealership was working on it with me.
Sell it and buy the one you want. If it's that clean, you'll have no problem flipping it.
BTW, welcome aboard!