Scat has several cranks for the FE, maybe other manufacturers too. A 428 crank and a modest overbore will net you around 416. That is referred to as a 410 motor and Merc made them for a couple years.
I don't know much on injection, Hotrod mag did a fuely FE build a few years back, used a Holley pro-jection I think. I know some bad reports on that system. I always thought a throttle body from a GM would be a nice street able setup.

Also on the aluminum heads, you should be able to run a point higher compression with them I.m told.
I drive a stock 390 every day. I really need to let it go for some better mileage but it's hard to.