The actual calculation for magic is this:

Damage = Spell Power * 4 + (Level * Magic Power * Spell Power / 32)

Ultima has a spell power of 150

From what you told us, Strago should be doing exactly 60,000. With the damage resetting at 32,768 like masamune1600 said (I also heard something like that...), you should be doing 27,232 damage and so should still be doing 9999 damage from the damage limit...

Ultima ignores defence, so it doesn't really matter who you use it on...

If you don't know your magic power, then we get something like this:

150 * 4 + (99 * Magic Power * 150 / 32) - (32,768 * 2)= 458
Some simple math and...
464.0625 * Magic Power = 65,394
So...
Magic Power = 140.91636
Let's say 141.

Now that you know that, plan your attacks strategically.

Take Bio for example.
53 * 4 + (99 * 141 * 53 / 32) = 23,331

It's well above 9999 and safely below 32,786. Perfect!
Flare might be better though, it'll give you 26,413 and it has all the perks of Ultima. And who says the strongest spells are always the best?