Well since no one has responded yet, and this is the second time I've looked at this thread, I'll have a go. Now I have nothing to base this off of other than my own thoughts/comfort levels. If it were me in my non-snorkeled 4runner (which has a 3" lift), I wouldn't go past the bottom of the doors. I think you would be pretty clear at that level. Don't try sue me if something goes wrong, but with that 4Runner, I've had the wheels completely underwater on multiple occasions and it has been fine. So that's how I got to the bottom of the doors thing, because that is lower than the top of the wheels (and mine has a mild lift compared to your stocker).
The other reason I would say don't go past the door line, is because in my other 4Runner (snorkel'd and lifted more than 3"), I've been over the hood (briefly) in water, and have had water come in and ruin some very expensive electronics. So even if the engine is good to go deeper, you gotta watch out for intrusion, especially if your gonna be submerged for more than just a few seconds. I think there are drains under the truck that will let water into the cabin too.
I know this was a lot of rambling but I hope it helps, if only a bit.
