advice needed for arduino as diesel injection brain...

One of the key factors for getting a well-behaved engine is to manage the fuel injection quantity accurately and repeatably. That's why people use fancy peak-and-hold drivers and voltage compensation and fuel temperature compensation and so on. A driver that barely manages to open the injector is going to put you at a real disadvantage. It sounds to me as if your driver is not providing as much current as you need, and if so you should consider uprating it.