Okay, I'm going to try and answer some of your questions. But firstly, a warning - you are asking logical questions to a film that has a 6.3 rating on IMDB, but perhaps more tellingly, a 15% rating on Rotten Tomatoes. It is incoherent and poor at times!
Secondly, I'm aware these answers aren't perfect, but given the length of time this question has been unanswered for, I feel they should be helpful.
So firstly, a brief plot summary (created after speed watching the film!) I know you know this stuff, but it should hopefully make it clear for other reads of this question:
Jinx ends up in the bank to complain about an ATM transaction fee that
will overdraw him. As he enters, he inadvertently walks in on a
robbery. Simon chases him into the vault and he accidentally locks
himself inside, only to realise he's not alone - Jessica is there with
Jessica is trying to open the safety deposit boxes using the vault
computer. Jessica can open the vault door, but Jinx won't let her and
refuses to be bullied by Simon. It's at this time the police arrive
and surround the building.
As time goes on, Jinx and Jessica realise they both feel they have
been used, so decide to escape together. During this time, between
contacting both Simon and the police, Jinx realises Nick is the real
mastermind of the operation. He is one of the bank's executives. He
hired Jessica to set an account up that would allow him to access to
some of the bank's money - but this could only be done under the
disguise of a robbery.
Simon knows nothing of this and is supposed to be paid by whatever is
in the safe deposit boxes. However, Nick can't execute his plan
without having an ATM card and PIN, which handily Jinx has. Jinx
agrees to let Nick use this if he and Jessica can escape and get a
cut. Nick agrees.
As they work on this, the police cut the power to the building. Jinx
plays a double bluff and tells the police that if the power is turned
back on, Simon will let two hostages go. He then tells Simon that the
police will turn the power back on if he releases a hostage and turns
one of his crew in (i.e. him and Jessica).
So now on to your questions.
Who shouts "you two stay where you are"? And why?
It seems likely this was Simon. Despite making the deal, he'd been made a fool of by Jinx and was getting more and more unbalanced as the film went on.
Who shoots Simon?
I've read/discussed two possible theories for this. The most likely is that Simon shot himself accidentally. Earlier in the film the gun malfunctioned and it's possible that it accidentally fired again as he tried to give it to his partner. Another possibility is that the stupid partner of Simon shot him, since he would have been able to see he was about to kill Jessica (and was perhaps confused by the situation)? Quite a waffly answer I know, but I think the prevailing opinion is that it happened due to the faulty gun. Do remember that right after this, Tip 9 appeared on screen ("Remember, shit happens").
Why do the police suddenly decide to storm the building?
I'm guessing standard procedure after having heard a shot fired.
I assume Nick goes through with the deal as Jynx is now driving a flash new car, but who is he on the phone to?
Good question. It certainly looks like Jynx and Nick are on the phone to each other. Possibly what we hear is their conversation from earlier and we are watching the "afterwards" and they are talking to other people. But this seems unlikely. I think they are talking to each other, although I can't back that up with anything other than by saying it seems logical.
I assume he's on the phone to Nick who is coming out of the bank. Why do they stay on the phone when they're right next to each other?
If they are on the phone to each other, goodness knows. Dramatic effect seems most likely. After all, most of the movie was spent with phone conversations going on. Why not finish that way?
If he is on the phone to Nick, why is he meeting Nick when he obviously already has the money (hence flash car and clothes and such).
Again, I've no definitive answer. Perhaps they needed to meet a few times, as they couldn't withdraw all the money at once?
Why is Nick in the bank? (if that is Nick)
He is a Bank Executive. That could give him a reason.
Hopefully that gives some indication, but there are lots of unexplained issues. For example, the movie ends with Nick revealing "Tip #10 - Know When To Walk Away". This is spoken in a fairly sinister tone. Is he simply reminding the audience that they committed a perfect crime and it's time to stop? Is he suggesting Jinx and Jessica will be "taken care of"? It's all up to the viewer.