Wrapped up my remote start saga this morning, figured I'd write an update. First off ABSOLUTELY MASSIVE THANKS to riceandpho for selling me a used unit at what is certainly below-market rate, and offering advice throughout.
I owe you big dude!
First off, addressing the THREE units I purchased before getting something that works; yes I was in fact correct to diagnose them as faulty. Who would have thought! Three units from two brands all bad; of course made even worse by the fact that both companies (I will name names here): Viper and Crimestopper refused to provide customer support. I'm not sure what was up with the Viper unit but the Crimestopper units, due to having identical failures (no signal from remotes) points to a bad batch. It makes me queasy to think about the man-hours wasted if this is a large batch of bad units. Anyway, both companies get 0/5 stars and can ********** for wasting a huge amount of my time and not even trying to work with me--even worse when the problem was on their end and not mine.
Anyway, I got the Compustar unit in, hooked it up which took all of five minutes because I had already tapped most of the wires in the car from the previous attempts, and hit the start button on the remote and the car immediately cranked. Of course it didn't start on account of the immobilizer, but sticking a key nearby the ignition allowed it to start, confirming another theory; you can bypass having a bypass if you're willing to ziptie a spare key up by the ignition.
In the end, because I got a bypass I didn't end up needing to do that. I do think I would recommend paying extra for a bypass because it will prevent your car from being hotwire-able. I live in a state with low crime and a county with zero crime, so this is not much of a concern but for some folks probably matters.
Moving on. Wires in the car were mostly easy to access with a couple minor exceptions. Accessing the lock/unlock wires required removing the dead pedal and left bottom kick panel, breaking a clip on the dead pedal. There was just barely enough room after unplugging the target harness and the one it was attached to to tap. For whatever reason, the wire colors DID NOT match the 4runner remote start guides that are all floating around. I ended up just rigging a GND wire and testing pins by trial and error till I located them. Simple enough.
Keysense wire; remote start guides show this color wrong as well. Actually I don't think it's "wrong" it's just that where it's most easy to access it's not the color listed in the guides. This thread:
How to: 4th gen '05 Remote Start Install
Shows how to locate the keysense wire.
Finally, rear-window-roll-down. Kind of a extra credit item but if you are like me you use the feature a fair bit. This took some experimenting and I ended up with getting the feature to work with a simple caveat; the car needs to be remote started before the button will work. This is okay to me because the scenarios in which I use it (store parking lot, walking up with items to stow), I can just start the car first.
The reason for this is I tapped the "window down" button. I know there is a better route but this was easiest for me as I'm only so-so at automotive electronics. The basic solution was:
[Compustar Brainbox] -> aux wire with negative trigger -> relay -> 12V+ -> window roll down switch wire
In other words, the relay takes in a negative signal from the remote start unit and outputs 12V+ into a pin on the window roll switch in the middle of the dash. I figured this out by jumping wires on the switch plug until I figured out which ones actuated the window. The relay was just a standard automotive relay, and because I never remember which pins are which on a relay I just sat there with my multimeter playing with it till I figured out the correct pinout for GND, 12V+, -trigger, 12V+ switched output. I'm sure there are a myriad other ways to implement this feature but this is what worked for me.
Hopefully some of the details in here will help anyone searching the forums for remote start help. BTW I would add that if any of this stuff sounds like too much for you, wiring up one of those 1 button units without door lock support or rear window rolldown, would be downright easy as there are vastly fewer wires to tap, and they're all directly within like 4" of the ignition cylinder.