Page 153 and 154 of the main book.
"For every 3 boxes of cumulative damage taken on a condition Montitor track, the character suffers a -1 wound modifier."

Does that mean that you take a -1 wound modifier when you take one point of damage or 3? The example doesn't help:
"... a character who has taken 6 boxes of Physical and 3 boxes of Stun suffers a total of -3 wound modifier."

I'm positive this has been discussed at length here, and a definitive answer has been reached, but I appear to have failed my Data Search + Browse Program appears to have glitched or something.

When you reach 3 boxes of physical damage, you immediately start taking a -1 penalty to stuff.

When you reach 3 boxes of stun, same.

What the example is saying is that the character has taken 3 boxes of physical (-1 penalty), another 3 boxes of physical (total of 6 boxes of physical for a -2 penalty now), and 3 boxes of stun (for a total penalty of -3).

So to be clear, if you have 1 box of stun and 1 box of physical, you take no modifiers, right?

Correct.

what he said...

To take a -1 modifier, you need to receive 3 boxes. Then for every 3 boxes you receive a cumulative -1.

Physical and Stun boxes are treated as separate, yet their modifers stack. [IE, if you take 2 stun boxes and 1 physical box, you DO NOT receive -1 modifier, but if you take 3 boxes of stun, and 3 boxes of physical, then you take -2 modifiers (1 from physical, and 1 from stun)]

And just to confuse even more, this gets changed to every 2 boxes if you have the Low Pain Tolerance Neg Quality...

And you can have a buffer based on High Pain Tolerance (Quality, Cyber, Adept, Drugs..), to confuse it even more.

And then there's the previously covered, if you have taken too much stun damage and are close to passing out, take off your armor so that you won't pass out, it'll just hit your physical damage track.

And probably getting killed or seriously wounded in the process.

Yeah really. Plus in the time you spend getting out of your armor you could be slapping on a stimpatch or getting the hell out of there.

I just figured it out! That's what Billy is doing at the end of Predator. His stun track must be almost full. (nevermind that he has some kind of geas that requires physical damage to activate his ultimate badassery.) And the effect of this strategy will likely be roughly the same in your SR game.

Really, the whole Troll taking off his armor to avoid passing out really bothered me when I first saw the SR4 rules. Eventually I realized that it is a theoretical problem that just never comes up, and I stopped caring. If you've actually had it come up in a game, I may resume caring, on your behalf.