Great project.  I have some empiric data for you to consider for both blend and fumigated ethanol.  Fumigated e85 you have to limit  to about 40% substitution (without remapping the injection timing)  before knock becomes a serious concern.   You can fumigate right into the intake via port fuel injection.  Common rail engines would be straight foreword to re-map for higher substitution, older mechanically timed engines would need a variable drive gear like Mack's Zexel pump drive (now owned but not in production by Bosch).

 
Another option is direct injection into the chamber. 
http://www.westport.com/news/2013/next-generation-high-pressure-direct-injection-system-hpdi-2.0

This injector would require downsized nozzles but it would get the job done.  I am not sure all what needs to be replaced (whether a replacement head for new style injector boss or not).  The only aftertreatment on these motors would be a cheap oxidative cat converter to clean up some of the ethanol VOC's.