Gary,
That's a nice drawing. It shows that you know what you're doing and have a great attitude about "getting it right."
I see two changes I'd recommend. First, because of the pulsing action of the PWM output, you will only get an accurate reading on your amp meter if it is located in one of the input legs of the PWM -- between battery and the PWM feed.
The second is on that PWM battery input feed. You don't show a HD relay in your drawing, but do list one in the parts list. You definitely need to use one. On the relay, there should be two large terminals. One of those goes to battery plus and the other goes to the positive input of the PWM. This line should be fused with a fuse AT LEAST twice as large as the amount of amperage you plan for the system to draw. I like to place my fuse as close to the battery as possible. This line is also where you want to insert your amp meter.
You will also find one or two smaller terminals on the relay. This is for the low amperage connection that will turn the relay on, allowing the main circuit to energize. If there is only one connection, apply 12v positive to it to turn on. If there are two terminals, then one of for 12v positive and the other is for 12v negative.
You should pull the 12 volt positive for this from the "run" side of the ignition switch. You can probably, as Jeff said, find somewhere in the fuse box to tap into this circuit instead of physically connecting to the ignition switch, but just make sure it is only powered when the switch is in the "RUN" position. DO NOT use one that is powered when the switch is in the "accessory" position. If you want a toggle switch on the dash so you can shut the system off manually, the switch would go in this line, not the main power cable.
As for wire size, that depends entirely on what amperage you intend for you system to operate. Provide me with that information and I'll look up the proper wire size in the chart.
Hope this helps,
Steve
1991 Plymouth Acclaim 3L V6.
1 dry cells with nineteen 6"x8" 316L ss plates, driven by constant current PWM set at 35 amps (13.3V at PWM). 28% KOH electrolyte. Total measured output 2.5 lpm. Mileage went from 18 to 26 mpg, all city driving (44% increase). EFIE set at .370 and I still need to play with ignition timing.