So first on the agenda... Battery wires. So one of the batteries have to power the drive motor ESCs. Would creating a Y-lead set be the best way to do so? Or is there a better way?
Yeah, I'd use a Y-Lead in this instance as it creates a independent part that you can add in the wiring for the drive system removable link. I'd use something like a XT60 Y-Lead as the connectors are super tight (not something you want to come undone during battle).

I also have doubts about using aluminium cans as a skid plate. If I cut them out, made them safe to handle then used them as the skid plate, would that work? Or would I have to spend some more money on buying some nylon?
I'd probably go with the Nylon here. You could add in several layers of cans to strengthen it but I fear it would buckle when suitably hit. A single block of Nylon (or HDPE, although that does scratch fairly easily) would be more resistant.