You should be able to get MIDI input with nothing but configuring the MIDI setup in the Apple Audio/MIDI setup. You shouldn't even need to mess with the environment to get MIDI input.
I would suggest you watch this tutorial up to the point right before the importing of the various multiset instruments. Then set it up accordingly on your computer.
Beyond that I don't have any direct answers but assuming everything else is done correctly what I would do is set everything up the way you mentioned, and after you shut down/restart Logic , restart the Maschine and when it boots up see if your MIDI input then works. This is a long shot since I am assuming everything else is in correct working order, but it's the only thing I can suggest without looking at it.