As usual, this is a huge project and rather than have the entire thing on here, I'll try to keep it short but try to get all the pertinent information included.
I have a mobile robot chassis with outdated electronics so we've gutted it and are replacing the control systems with a Raspberry Pi and two Arduino Megas (don't ask why, please). The Pi acts as the brain, one Mega handles input sensors and the other Mega handles output to the motor H-bridges. One of the Megas also has a clock signal that syncs all three devices together. So, since the Megas startup in ~1 second and the Pi takes significantly longer, I've added this to the Megas: while(some_pin == low) {} and when the Pi is ready to start, it sets that pin to high.
This works fine except occasionally, maybe 1 in 6 times, that pin will go high and the Megas will start going before the Pi is ready.
So, the first question (and only question if there's a good answer) is simply: are there any GPIO pins on the Pi I can use that are guaranteed to stay low during the boot sequence?