u need to replace ur Stock Boot.img into zip folder. Just open with 7zip and drag ur stock boot.img into 7zip window and click on yes.I wonder why problem exit in first place. I mean i'm sure it work for other people here.
Anyway, i don't understand what you mean exactly, do you mean to say replace boot.img after flashing miui with stock firmware boot.img? or replace boot.img before flashing miui if so replace with which boot.img?
Then Flash it or ur can flash it like its and are after flashing this MIUI just restore ur boot.img form adavnce restore option from ur recovery it will do it for u.