The best way to determine how much cable you need is to take some rope & follow your factory wiring and add about 3 to 4 feet. Sometimes the bigger wire & split loom around it won't go exactly where the factory wire went.
I'm just about finished with my upgrade (waiting on the 200a alternator) and I'll post some pics pretty soon.
I've read where some people use a 200a fuse/breaker while some use a 250a fuse/breaker for a 200a alternator. I've got both 200a & 250a fuses, I'll probably start with a 200a fuse to see if it blows under full load before I drop in a 250a fuse.
It's a REAL GOOD idea to upgrade your ground wires when you do the power wires. Ground engine to frame, frame to body & body to battery.
Your circuit is only as strong as the weakest link.
I used the knukonceptz 1/0 awg aluminum/copper wire (check my profile for a link to the threads). It seemed a little stiff to me, but I had to make some tight bends with it. It is only about HALF the price of 100% copper wire.