I feel you, I had a lot of problems mapping the controls to a more familiar style as well.
Here's what seems to work for me now:
For throttle, remap it such that mouse wheel increases/decreases throttle in 10% increments (and not the default 'smooth' or 'linear' or whatever it was called), and map some keys at your convenience for 50%, 100% and 0% throttle (z-x-c perhaps).
Frame-shift-drive, map to either 'j' for the X-feel, or spacebar for practical convenience.
Mouse adjustments:
Remap it such that the mouse axes control pitch and yaw, not pitch and roll. I found that decreasing the sensitivity to like half the default improved the feeling (though I use a high-dpi mouse, your preferences may vary a lot).
Put Q and E as roll left/right buttons.
Change wasd to strafe up/down/left/right.
For the rest, just make sure you set the 'cycle next target', 'select target ahead', 'deploy landing gear', 'deploy cargo scoop' buttons at your convenience (for landing gear and scoop, I suggest something on the numpad or around the 'l' key, so you don't accidentally hit them).
And leave the 'docking controls' section empty, as that is merely meant to be an override whilst at stations - with this scheme, you won't need any overrides (until you get to a superhuge ship that literally needs to have an axis-controlled roll instead of a button-controlled one, but by that point you'll be comfortable enough to pick what you like best yourself).
That will, I think, give you a mostly X-feeling controls; You will have to get used to the mouse turning your ship sort of via a vector offset and not explicitly (so you have to re-center the mouse back once you've done turning), but with it being yaw+pitch, it won't be as hard. Just keep in mind that turning side-to-side is really slow, so you will want to use the q+e as much as you can.
I think you won't have to change anything else, the qe+wasd+spacebar will also control all the in-ship menus.