"If every strike is a block and every block a strike, when do we inhale?"
After the exhale....

!!!!
All joking aside, you'll learn through experience. As you continue to progress through the system you will begin to see, more clearly, the difference between major and minor strikes.
As an example, we'll look at alternating maces. If you "kiai," or exhale completely with every move then you won't be performing at an optimum level and the technique will be sluggish and ineffective. You should try to examine what the strikes are doing. The first two inward blocks are striking to the radials (if possible), but their function is to redirect the incoming push so you don't eat it. These first two blocks roll rather quickly and end with the back-knuckle. The motion is similiar to the one congo line dancers make with their hands, or the same motion as the one made when singing "roll the gospel chariot along" from bible camp (whichever helps you learn it best). You can use a timing phrase like, "bud - da - Whaaack" for the first three movements of the technique. It not only gives you the timing, but the point of emphasis as well. By actually saying it while doing the technique your following the right breathing pattern.
Make a phrase for the last part of alternating maces, then see if you can make up your own for the other techniques. If you don't feel comfortable saying it, then just change it to some type of groan or noise that you would feel comfortable doing, but give it a shot it will help you with your breathing.
p.s. Depending on what technique I'm doing, I'll inhale after recoiling from a major strike, but most of the time I can do the techniques on one breath. By the way are you one of John Haag's students?