I am also stuck with the same problem . I have a custom lookup component with lightning:input . i want to pass this value to the lightning:inputField via value attribute. but it doesnt work. So now i have to pass all the inputfield values to a aura:attribute with sobject and pass it to apex for doing DML.

Since i am not able to add a comment, i am posting it as answer. apologies !

Spring 18 : Value Attribute in lightning:inputField

Not sure if you are running into same issue. but i have a solution. please do check