Just went thru a similar issue, diagnosed with assistance from the guys at Hillsboro diesel. My jakes were flaky, sometimes wouldn't work - other times would work well. I thought it was the buffer switch, I had them replace that and it didn't fix the problem.
This was the fix for me: Use an ohmmeter and measure the resistance of the wires that go to each head separately - measure between the wire and ground. You need to disconnect them from the buffer switch to do this. I found the inner head shorted to ground. That was causing both sides not to work properly. Of course that was the least convenient side to get to, so I was able to disconnect that side and run on half jakes until I had time to pull the turbo and valve cover to investigate. One of the coils was shorted internally.. again diagnosed with the ohmmeter. Replaced the coil myself, and all is well again.
It could be any number of things, a short, an open, in the wire, a connector, or coil. The ohmmeter is your friend to find it.
If you pull a coil, there may be a small o-ring at the tip of it. Make sure you know where it went - mine stayed in the hole. I had to use a mirror and flashlight to see it.
Scott
'69 4107
Gladstone, OR