Preserving WYSIWYG LUT input assignments

The actual inputs used are a function of the router. That being said, the routing variation is usually larger than the variation of inputs through the LUT, so unless you lock down the routing, I don't think just locking the LUT inputs will work. Make a copy of your design and go to Assignments -> Back-Annotate and lock everything down to the routing level. The syntax of the .rcf is pretty good, and it supports wildcards, so you might be able to pull out the routes you need.

Note that the .rcf does not drive placement, i.e. if the placer doesn't put a LUT in the right spot, the .rcf is useless, so you'll need the placement assignments for the nodes you're working on in conjunction with the .rcf.

How tight of control do you need? Have you tried timing constraints to drive it? The nice thing is that the fitter has the D5 and D6 delay chains to help dial in a value. Also, you could just lock everything down and manually assign D5 and D6 yourself.

What you're trying to do is very difficult. Besides fine-grained control, you need to work with and understand the fitter, the timing models, etc. Good luck.