Jahred,
I'm not real good at diagnosing stuff like this without seeing the parts. Heck, I'm not real good at diagnosing....
The function of the shim, as I understand it, it is not to control the depth of engagement but to allow the starter teeth to retract away from the flywheel enough to completely
disengage. If they don't completely disengage, metal will be ground away, usually with some considerable sound effects
Don't ask me how I know this.
As to the auto/stick flywheel differences, I'd suggest you contact that starter vendor (or one similar) and ask that question.
With that much metal disturbed (if I'm visualizing the pinion gear's damage correctly) there may be some damage to the teeth on the flywheel. You may wish to inspect there before you try another starter.
Ouch!
Tom