These should be pretty easy to fix. The non alignment of the cannon first: You will find a curved slot that holds a switch on the bottom of the cannon mechanism. You will also see a switch that is pressed by a post off the bottom of the mech. The one hitting the post is the home switch. You will need to change its angle so it is tripped when the thing is aligned. All you need to do is lift the play field with the cannon in the 'home position'... currently out of alignment, and loosen that switch and twist it by a small amount so it activates later/earlier as needed. Tighten again, and then start the machine. It should home now. Repeat until you get it right. See pic attached for switch I'm talking about. Once you see it, it will make sense. I'll bet yours is just loose. You might need to change the position of the one in the curved slot too. That one controls when the thing reverses.
As for the flippers, assuming the flippers themselves are responding the correct button, it sounds like you have the wires on connector J110 reversed. Not sure if the orange or the white ones or both, but that is where the flipper signal is sent to the switch matrix / CPU. I've attached a screen shot of the proper positions for the wires on this connector. If they are wired like this, then check these wire colors where then enter the CPU board in the little plugs toward its bottom. They could be reversed at that end.
Good luck. This is a great machine.