Shoddy Install (what to fix?)

I knew my roofer had done a sloppy job, but hoped it would be watertight. Unfortunately, almost immediately we had some visible leaks around the chimney and plumbing vents and I wonder if there's more subtle water intrusion that will do damage over the longer term. I have already installed the plumbing vent boots and have ordered materials to properly flash the chimney. I'm wondering about the following issues that aren't causing visible damage (yet) but I worry about:

• There is no overhang on our flying gable so water just runs down the facia. Will adding a couple of inches of panel overhang suffice?
• The panels were overlapped incorrectly, should I unfasten them and swap the overlap?
• He didn't follow the proper screw pattern, but will it do? I don't really want more holes in my roof.
• Nearly every screw is overtightened. Should I replace them or wait for them to fail?

He didn't install inside closures at the eves so I'm already planning on doing a fair amount of unscrewing to install those (luckily/unluckily no butyl tape was used in the project so things should come up easily). Happy to do whatever else I can to try and fix this roof up. We spent a lot on it with the idea that we wouldn't have to worry about roof issues ever again!!

roof pics copy.jpg