In that particular situation, there is not much more you can do. We often don't work in the pristine conditions of MLB umpires. The lighting, field conditions, weather conditions, often affect our games. That's a long way for a human to see the flight of a small off white ball.
The only thing I can see that could have been done differently is that your partner could have gone out on that ball. IMO, it's a good idea in that situation for your partner to read this as a trouble ball and go out. I'm in no way faulting you or your partner. I'm not even sure you could have got a better angle on a ball hit like that, either.
We just have to do the best we can. It's really hard to see a ball hit over a chain link fence, especially at that distance. Maybe wait a tick before calling a 2 base award? See the actions of the fielders first? If they don't throw their hands up, then use that information to your advantage.
And yes, I've had trouble with balls hit over chain link fences. Don't beat yourself up.