I'm all for muscle memory and had the same issues as the OP. The thing that helped me the most, in addition to the fundamentals, is a section in Brian Enos' book "Practical Shooting". It's a competition book but has tons of useful info for any type of shooter. Overall, I strongly recommend this book. It's a little heavy reading but absolutely worth it. Brian Enos has given me permission to quote his book directly. http://www.brianenos.com/store/home.html
Don't forget to use an unloaded gun when practicing these. From Page 169-170. Section 6: Development:
I strongly suggest that you spend whatever time it takes to progress through these exercises. I think that developing the intuitive awareness these will help instill in you is critical to reaching your potential. Because you'll acquire the skills in increments...do these exercises in order. Make sure that you're completely satisfied with your ability to do each preceding one before you move onto the next...Don't attempt to do these exercises to gain any certain result because you're not going to gain any result that's joing to be immediate enough to even matter. Just pay attention to what you're doing and how you are feeling and eventually your body will start following your own images.
Start by holding the gun with your normal shooting grip and aiming at no place in particular. Lower the gun. With your eyes closed, raise the gun to what you feel is your normal shooting position, then open your eyes and verify sight alignment. Keep practicing this until you can raise the gun and always have the sights appear when you open your eyes.
From that exercise, you'll move on to starting with the gun in either hand so that now you'll have to assume your grip before raising the gun. You again aim at nothing particular. You can start with he gun in an aligned position, then take the gun out of your hand, reseat the gun, close your eyes, mount the gun, and see if you can verify sight alignment"
He has a couple of additional steps but this is where I'd want to send you to the book. My own take is even before Exercise 1, try this: get into your grip & stance, aim at no particular spot on the wall and just verify your sight picture. After you get your sights aligned, just close your eyes and keep them closed for a couple of seconds. Open them again and see if your sight picture is still in place. Keep practicing this until your sights stay in alignment. If they do, try and keep your eyes closed a little longer, or move onto Exercise 1.