Yes, EFI can be used successfully with virtually any motor and provide near perfect a/f ratio under all load, rpm, and atmospheric conditions, even on radically cammed or boosted engines. However, they do require some time to setup because there are many parameters that must be tuned for your custom engine to run correctly all the time. You or your tuner will need to become very familiar with programming whichever ECU you decide on and will spend a solid day or two on the dyno ironing out the basic fuel map. From there plan on some on-water sessions to sort out driveability issues such as in/out gear idle settings, acceleration enrichments, temperature enrichments, etc. It's a lot of work but when you're done you can have an engine that runs nearly perfect all the time. I'm using the Electromotive (http://www.electromotive-inc.com) stuff in my boat.
-brian