I wanted to respond to this earlier but I didn't have time. I've done some of these cars; I'll throw a few comments on here:
1. The tech sheets from the alarm companies will have you running wires all over the car and making a mess. Here's where I go for my wires on that car:
1A: The harness going up the steering column has not only all your ignition wires, but more: horn, negative parking lights, and door trigger. You'll notice there's an illumination ring around the key cylinder...that light comes on when any of the five doors are opened; use that as your door trigger.
1B: Tach at the OBDII plug below the fuse box.
1C: Brake is blue at the fuse box; easier than going to the pedal, and less chance for the wire to get tangled on the pedal. Various blue wires at the fuse box; test until you find the right one.
1D: Doorlocks in the harness in the kick panel that comes in through the door.
So....you'll end up with a nice clean install, going to only four locations in the entire car.
2. Your ignition wiring above looks MOSTLY right. The only two things I see are:
2A: As Mike said, how about the second starter wire? If I'm correct about the Viper, you should be able to connect the pink/black flex wire to it, and then go into programming and program it to act as a starter output.
(You only need to interrupt ONE of the Toyota's starter wires to perform anti-grind/starter kill; I recommend doing the interrupt with the Viper green and purple on the thicker of the two Toyota starter wires.....connect the pink/black directly to the thinner starter wire without interrupting it.)
2B: The accessory wire in that car powers the radio, power mirrors, cigarette lighter, and other non-essentials. If it were my car, I'd prefer to keep the radio off during remote start, so you don't disturb the neighbors, and so you don't lose song on the CD your were listening to when you parked. Just my opinion...go ahead and hook it up if you prefer. But anyway, the HVAC system on Toyotas is powered by one of the two ignition wires.
3. Just like the others said, ignore the factory keyless entry and leave it alone; it won't hurt anything. I've seen some people like to remove the batteries from the OEM remote so you can't trigger the aftermarket alarm by accident.
If it were my car, I'd store the OEM remote keys until resale time, and just use the valet key, or get some nice non-transponder, OEM keys with logo made at the Toyota dealer.
4. You were asking about that auto-relock feature from Toyota. The Viper won't do that by default, but it is in the menu as a programming option. Up to you.
5. You said you'd prefer to unlock all five doors at the same time, instead of driver's priority, right?
The quickest and easiest way will be to just connect the Viper's green and blue wires to the car as normal, then go and program the Viper for double-pulse unlock. Also, program the Viper's doorlock pulses for 0.4 seconds instead of 0.8; it'll open the passenger doors faster this way.
If you really wanted to get fancy, you could do something different: First, find the wire in the kick panel that comes from the unlock switch on the driver's door panel.
Then, take the Viper's blue unlock wire, and split it with two diodes. Connect one diode to the unlock-switch wire you just found, and connect the other diode to the key-cylinder-unlock wire that's listed on the tech sheet.
This will allow the Viper to unlock all five doors on a single pulse, which allows your passengers to enter the car a little more quickly.
There's only one other thing I can think of I'd do if it were my personal car and I had the extra time.......
Turn on the hazards and listen for the factory flasher clicking on and off. When you locate it, look for the negative hazard flasher there.
If you connect your GREEN/ black disarm and GREEN / WHITE rearm wires to the hazards, you'll get flashes when you lock and unlock, similar to (but not exactly like) the factory setup. It'll also flash at remote start startup and shutdown.
If you're not going to be using the Viper's horn or dome supervision output, you could take advantage of either of those to flash the hazards if the alarm is triggered.......
If using domelight supervision wire: Connect to hazards; program Viper for "ignition controlled domelight off"
If using horn wire: Connect to hazards; program for your choice of horn-honk with lock/unlock on or off. (Note: you could program it for horn honk on with locks, then DON'T connect your arm/disarm wires......now you'll have hazard flash on lock, unlock, alarm trigger, but NOT with remote start.)