Assuming they gave you the right pipe.......
The best way to fix it is to find somebody with an acetylene torch.
(propane torch's won't get hot enough)
Lay the bike on its side.
Disconnect the rear "hanger mount" of the pipe.
Bolt up the front mount (to the cylinder). nice and tight and inline.
Then heat the header pipe (up near the cylinder) all the way around, till it turns an orange color.
Then grab the back of the pipe and bend the pipe till the rear hanger mount lines up with its bolt hole (and you may have to drill a new hole).
That is the correct way.
The problem will be finding somebody with a torch who will do it for you.