As for your spare ball, I wouldn't worry too much about it going over the thumb hole. If you watch Walter Ray throw at 10 pins, his ball clips the thumb hole at times. I do the same thing but as long as I hit the spare, I don't mind.
I had the same problem regarding hitting the thumb hole on my strike ball. What helped me is my coach started me on the 1-step approach. Step and throw the ball. It made me realize in what position my hand should be in when it left my hand. Can't really offer you more than that. If you can get someone to watch and/or video tape your game, perhaps you can analyze and fix the issue. I'm lucky to have 3 USBC silver level coaches that work in the house I bowl at.
Good luck.
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The bowler formerly known as BrunsRod.
Solid 7 Pin?? 299 Game??!! WTF