If somehow, you had an injector stuck open, on compression stroke that cylinder could force compression pressure backwards through that injector into the injector pump. I know you had the injectors rebuilt, but it's just a thought.

 

The return lines are more or less under a little pressure so any leak should leak out not suck air in. I agree with your feelings of nothing ventured nothing gained. I too am learning about this little "b" engine and it is very similar to the "c" engines but not exactly the same. So as I implied earlier I might be wrong on something but I bet I will still be in the ballpark. If you have not already done so, take a look in the Tech article thread, there is a post on turning up the VE pump. It has several good cutaway pics. These might help you understand what is going on and lead to a diagnosis.
How about the gear timming issue I asked about? I remember that cost me a whole days work chasing my tail one time.

 

torque fan...that sounds like a very interesting scenario. I bet you might have it !!! I have had problems with air only after the injectors were rebuilt. I had the #4 cylinder such that it would never bleed out. sometimes before it would only crank when I had all the lines tightened except for #4. I only had thought of it in such a way that the leak was looped in the fuel system. I havent tried completely undoing the line to that cylinder. I can't wait to give it a shot. Will have to wait til after work tomorow though. thanks.

 

I verified a stuck-open injector by removing it from the engine, and putting the tip in a glass of water. Blow into the end of the injector, and look for bubbles to form in the glass.

 

Very interested to see how this turns out. I installed a new pump n everything checks out except the running part. Did run on its own for a brief moment, may be indexed wrong