The easiest thing to prevent the wear of e85 is fill up with 93 oct every couple fill ups of e85 and run it.
Is there any issue with residual 93 pump gas in the tank not being used up before putting the E85 back in? i know Shaun's e85 tuning includes a tune to empty out the tank with a key power on that way you can easly fully empty the system.
Also, the issue with the 47 injectors was not duty cycle it was tuning. the 47's dont have fuel tables published yet so i think there is an issue tuning them. ID1000's are awesome for tuning and will support any future mods.