The only thing stopping you from using a larger battery is the tray. There are a few companies that make larger trays for dual batteries.
The extra wire is there so you don't blow the alternator fuse in the Power Distribution box. Currently there are two 50A fuses. If your alternator has to charge a dead battery it might push more then 100A through there. IIRC, you can use a #8 gauge wire and should be okay for an additional 85-150A. Although I've seen some say #10 is fine up to 200A. Keep in mind that the length of the wire has to be less then 4' or else you might need to go up a gauge.