This seems to be a general problem. Over time, one accumulates certain habits in hands and arms that will result in the corresponding muscles to adapt accordingly. Hands and arms will develop differently in terms of dexterity and general capabilities. After a while, these differences become locked into the physiology. Also, if you do most of your daily routine (writing, picking up things, holding things, etc.) primarily with your right hand, the muscles in your right hand and arm will be tighter than those in your left hand/arm.
It will take some time to get this corrected again. I had a similar experience after recovering from an injury. Whenever I observe my hand doing something "bad", I slow down and "tell" it to do the right thing. I repeat that a few times, always making sure that I do it slowly and that I am fully conscientious about it. So tell your index finger not to stick out; play your scales slowly; gradually increase the speed. It's almost like psychokinesis!
It's often hilarious! If I, for example, have a finger curled more than I want it to, I tell it to uncurl. The finger reacts very reluctantly at first, like a little dog that doesn't want to sit down. It's like a little fight of mind over flesh. Eventually, it will obey.
It will all come back slowly with time. Good luck!