. . .if he is going to pass

[jutfrank]

It makes more sense to me to think of 'be going to' in this context as predictive. There's a predicted real future outcome: he passes, and then there's a future prerequisite condition: he gets his act together. I don't think it's at heart about intentions.

 

[emsr2d2]

1. He will pass if he gets his act together.
2. We only know that he wants/desires to pass.
3. We only know that he intends to pass.

 

[teechar]

What do "is going to", "wants" and "means" express in the sentences

Please note that "going to" here is not about intention at all. It's about likelihood. It's an entirely separate and different meaning.
I'm going to sell my car next year. [ Intention]
It's going to be very hot next week. [ Likelihood]

going to

intending to do something in the future, or being certain or expecting to…

dictionary.cambridge.org

So,

1) "He needs to get his act together if he's going to pass."

= He needs to organize himself (prepare well) if he is to have a chance of passing.
And of course, you can turn that around (as @Annabel Lee has explained above), and you'll get:
If he is to have a chance of passing, he needs to prepare well.

2) "He needs to get his act together if he wants to pass."

That's just a straightforward zero conditional.

3) "He needs to get his act together if he means to pass."

That's not natural.