Why did his boss and the girl go to all that trouble?

I have the same question.
She tells the boss that she did not have the opportunity to kill him at the Diner, so it does not seem mandatory that she use the weapon for the kill.

I also don't know why the boss was there at the end.
It doesn't seem like something the boss deals with himself

I was born in the house my father built

The only explanation I can think of his she really did need the gun for some other job but then when he quit his boss sent her after him instead.

I thought it was all a bit elaborate too. And when he arrived in rome, I didn't quite understand why his boss knew about what had happened in Sweden. When they first spoke on the phone he sounded surprised to hear from him, like they had not spoken in a while.

It may have also served the purpose to make us see how alone he was - the only person he could trust wanted him dead, and so much so went along to the parade to make sure the job was done.

This script never resolved the plot. You may call it ambiguous. I call it lazy, dishonest, sloppy etc.

Also, it's not remotely credible that a character in the protagonist's position wouldn't be wearing a vest that protected him against torso gunplay.

Also, it's not remotely credible that he kept calling from the same public phone. You get away from that after week one of training.

I think the boss was the one behind the Swedes. Clooney didn't know that at first, but perhaps got a little suspicious when his boss then sends him to a very small Italian village with a cell phone (that can be traced). Clooney chucks the phone and goes to a different, larger, more easily hideable town. I'm guessing the boss thinks Clooney has served his usefulness and need to be made quiet.

He takes the next job, perhaps he needed some money, or perhaps he wanted to test his boss? I think the boss did intend to use the sniper gun for another hit. Sortof, killing two birds with one stone thing. By meeting up with the client, the boss is able to get an idea where Clooney is hiding. He then points the Swedes in that direction to track him down. Clooney, dodging another assassination attempt, is now convinced his boss is leaking his whereabouts to the Swedes. He tells his boss absolutely "he wants out" hoping perhaps that will save his life, but after the conversation, he has a 'gut' instinct that the gun he is now building may be used against him, so he 'adjusts' it.

It did seem unlikely that the boss would try to finish it himself, but maybe he too had a gut instinct that Clooney was on to him and might 'adjust' the sniper gun.

I agree with your explanation. what made no sense is why they would try to take him out while he is standing in a crowd with the whole village as potential witnesses. It is not like they had to kill him that instant. they could've waited until he went back to his apartment and killed him when he got out of his car or opening his door with no witnesses around.