Metal Claws is only good to save a spot for Slash at lvl 44. Switch out Scratch for Cut when you get the chance. Flame Thrower replaces Ember.
Wing Attack is actually really useful, so try and keep a flying attack. That or Aerial Ace. Don't bother with Fly, that's what you've got Pidgeot for later.
Onix will destroy you. That's why you needed Mankey. He sweeps the gym when you've got Charmander as a starter.
Get yourself a water type. There's a Magikarp for sale in the pokemon center before Mt. Moon. Worth the $500. Grind it til you get a Gyarados, and it'll save you. Dragon Rage.