This idea is not so far fetched. Before you hang me, let me explain. Here is what I am pondering. I know many guys with gas vehicles that need to run stand alone fuel injection systems. Why couldn't we do that with a diesel engine? I know that a mega squirt can be used to run fuel only ( not spark ) , all it needs is a tach signal, so the control unit knows where the engine position (timing) is. you might need a crank and/or cam position sensor and maybe a manifold air pressure / vacuum sensor.

So , quickly thinking about it, we would need:
The stand alone engine control system.
electronic injectors
electronic fuel pump(s)
Fabrication of a fuel rail, maybe injector adapters, maybe a toothed wheel for the crank
Wires, etc.

you would ditch the factory injection pump, lines and injectors.
the electronic fuel pump(s) would feed the fuel rail,
you would take the tach signal ( crank/cam sensor signal ) and the MAP sensor and feed it to the control unit.
then the control unit would send a signal to open and close each injector.

Its that simple. the only thing is that you would have to program the fuel map.

This would open up a world tunning options.

A quick search on ebay for "stand alone diesel injection" and I found:

http://www.nexumresearch.com/Commonrail.html

http://www.mwfi.com/fass/fass.html

the second link shows that these are replacements for some vehicles, but the idea is the same.

this is just a quick idea I gathered in 3 minutes while I posted this. If we think about it for a few days and research it, I think it could happen. BUT it would have a price tag, probably somewhere between $500 - $1000, However the benefits would be great. This would be great for people would want to run crazy boost levels since you are directly controlling the fuel delivery.