You've got me thinking now.
You need to inject the fuel in advance of the valve opening so that there is fuel in the manifold when the valve opens. If the exhaust is tuned right, then the back pressure from the exhaust will suck in fuel & air before the piston hits TDC due to the valve overlap - rather than sucking in air only. Unless, that is, your mechanical people have got a nifty idea about charge stratification. I would use a higher fuel pressure, and reduce the injector duration to get the mixture closer, and reduce the time between the cam sensor signal and the injection pulse start. That should get the mixture closer over a wider rev range (assuming you need a wide rev range).
If you're really going for efficiency, I'm suprised that you're not using direct injection - but that can get a bit dodgy as you need much bigger fuel pressure. Cylinder head mods are expensive too.
To get a few ideas about fuel control have a look at www.lumenition.com. I also have a few technical articles about fuel injection / ignition control using (amongst others) the 8051 (Just to make sure I stay on subject). If I can find them I will mail them to you.
Cheers,

Richard.