Yes, unless you are exclusively a reliever, don't go from the stretch all the time. You lose velocity. As for rebuilding your motion, I wouldn't do that so much as do alot of drills that overemphasize what you are trying to do, and then go back to your regular motion, which will be changed. Take what Barry Zito did this winter for example. He wanted another 6 inches on his stride. So he created a wierd delivery that game him another foot on his stride. Repeat that a couple hundred times, then go back to your regular motion, and bam, he had that extra 6 inches. Thats the key to changing your motion, overemphasise what you want, then do things so they feel normal. You will see a change.