How can I use Scavenging Ooze's abilities to save it from a Lightning Bolt?
The way to save your Ooze is to activate the ability one time. Two things can happen:

your opponent casts the Lightning Bolt. You respond to that by activating the ability two times; they'll resolve before the Lightning Bolt resolves, and your now 4/4 Ooze isn't killed by it. Then, the first activation will resolve and you have a 5/5 Ooze (with 3 damage marked on it).
your opponent does nothing, and the ability resolves. You have a 3/3 Ooze, and activate the ability one time. The opponent could cast Lightning Bolt while the ability is on the stack, but again you activate the ability one more time, that resolves before the Lightning Bolt does, and just like the first case, you'll end up with a 5/5 Ooze with 3 damage marked on it.

(If they don't cast Lightning Bolt at all, which is probably the best decision for them, you can activate the ability a final time.)