I think 4016 and 4017 can be read differently for different input devices.
ie: You need to strobe to read from joypad (to get all 8 bits), but you can read directly for a lightgun (especially since theres only 2 values really)
So maybe you could create a custom connector running from the cart to the controller inputs.
From what I've read here
http://wiki.nesdev.com/w/index.ph... you'd be able to access 5 bits (so not 2-7 like you initially wanted).
Al