When I have a bait that is not running true, I mess with the eye of the crank. Generally if the bait is turning left on your, turn the eye right and vice versa for the other way. you generally don’t want/need to move the eye much at all to get the desired correction to the bait. As you mentioned in your post, there is not an easy way to see if your correction is having the desired effect until your try it in the water.
I have not messed with any of my cranks too much in the modify portion. I have shaved the bill a little to get a little deeper and to cut the weeds better. In all of my attenmpts, you make the changed/filing/cutting to the crank and then you are going to need to make the correction to the eye of the crank to get it to run true.
I would careful in regards to cutting/shaving the bill too much off the deeper diving cranks. These bills generally are positioned to allow the baits to dive, off kiltering the bill to much could permentantly effect the baits running even with all the adjusting you do with the eye.
Just my two cents.