Clogged line

There could be a clog in the lines feeding some of the sprinklers, or clogged up sprinkler heads.

• Remove all the sprinkler heads (the procedure will vary based on the type of heads).
• Inspect and clean the heads.
• Turn the system on.

If you don't notice any dirt or gunk coming out, and the pressure does not increase in the low flowing outlets. Cap the working outlets, and turn the system back on. If you still don't notice a difference, you might have to dig up the lines to inspect them.

Damaged line

The line feeding some of the sprinklers could have been crushed, damaged, or broken.

• Cap the working sprinklers.
• Turn the system on.

If the pressure in the low flow heads does not increase, you'll likely have to dig up the lines and inspect them.

Not enough pressure

It could just be that the system does not have enough pressure for all the heads to work simultaneously.

• Cap one of the working sprinklers.
• Turn on the system.
• Repeat.

If each time you cap an outlet you notice the pressure increase in the low flow heads, it could be that there is just not enough pressure to operate all the heads at once. In this case you might have to have the system split into zones, and only run one zone at a time.

To answer my own question after solving the issue...

If the problem is only at the last two heads and the first ones are fine, then it is definitely a problem occurring after the first heads and unlikely to be valve-related (though not impossible). A broken line is most likely in this case, since your last two heads are dry in the risers and flex lines (it's not the heads merely being clogged). Broken pipes can usually be revealed by looking for muddy soil after running the zone for several minutes, especially if it's a break so bad it is completely stopping your last two heads from receiving any water pressure at all. If the soil has become impacted inside the broken pipe it may be difficult for the water to escape and reveal the break.

One common method to this problem is to increase the water pressure to the break and force the water out. It will not be so much pressure that damage can be done to the PVC joints and heads (as it will only be for a few minutes nor will the PSI be any higher than the output of your main water line or jet pump). This increase in pressure can be done by capping off all the sprinkler heads in the problematic zone. This will put more force on the possible break and on the soil that may be clogged in the pipe. After several minutes the leak may reveal itself. I'm sure there are several ways to cap off sprinkler heads, but the most common and simplest method is to buy PVC threaded caps (3/4" or 1/2" depending on your risers) that screw right on to the risers.