Butter,
You sure do ask a lot of questions!
The muscular asymmetries you mention are not surprising. They are simply adaptations to your activities. Unless you plan on learning to pitch left-handed, they will most likely continue to some degree as your activities are not symmetrical in nature. There is also no reason to assume that you are more prone to injury because of them. An easy way to approach this in your strength programming is by using a lot of dumbbells for presses, pulls, etc. If you work unilaterally, use the "weaker" arm first.
In your case, I'd be more concerned about overuse type injuries, so keep track of reps and volume of skill work just like you would for strength workouts. There should limits to number of throws, swings, and intensity of skill work to allow adequate recovery.
Most pitchers will test positive for an instability (based on standard tests) simply because of the extreme range of motion required to pitch at high velocities. If you've ever seen a pitcher throw on high speed video, you'll see what I mean. That doesn't mean that you are unstable at high velocities (specific adaptations to imposed demands, i.e., the SAID Principle). If you have pain, then of course that needs to be addressed.
Along the same line, increasing strength at slow velocities will not necessarily guarantee increased stability at high speeds. That's why throwing progressions, pitch count, preventing fatigue etc. are such important factors even for young pitchers.
Your best bet would be to train your body symmetrically and get some really good coaching from a pitching standpoint.
Also something to keep in mind... throwing velocity and strength are not highly correlated. They are at opposite ends of the force spectrum meaning the strongest guys in the world are not the fastest throwers. Be certain that the strength you acquire does not reduce your velocity. That means "bodybuilding" style routines are out.
Why do you have a "bad" ankle...diagnosis?
How old are you?
Bill Hartman, HARTMAN Certified
P.S. another thought...are you a starter or relief pitcher...the training would be different.