I am (well, my GC is) building a new home.  I could use some advice.

The roof is Galvalume.  We also have three direct vent fireplaces with flues that are to go through the roof.

Long before the roof was installed, we asked our GC if the fireplace vents shouldn’t be installed first so the roofers could work around them.  He insisted that it wasn’t necessary, and that the fireplace installers could install the flues after the roof was installed.

We had multiple conversations about how this was up to him as means and methods, but that the final result had to be right.  We also told him that we wanted the roofer involved so that the final work would be covered by the roofer’s warranty.

Well, our GC wasn’t there when the fireplace company came to install the flues.  Apparently someone from the roofer was, but it’s not clear whether he had any input as to what was going on.

They look horrible.  First, they’re not properly aligned or equally spaced – and there were no trusses in the way.  Second, the holes are irregular and show pitiful workmanship, in both the roof decking and in our brand new Galvalume roof.  Third, the gaskets cover poorly so in two places it is possible to stick a finger out into the open air – but for a dab of silicone.  And that’s not even including the debris they left in the attic or the fan duct they damaged and left hanging, which is minor in the scheme of things but a real additional irritant given how badly they screwed up the job.

Our GC is insisting that that the installation was proper, that all we need to do is move the misaligned chimney and tweak the angles and heights.

This just can’t be right.  I’m don’t know what I can do – other than to reject the chimneys and roof and, if our GC doesn’t properly fix it, hire someone else to do it.  And I don’t see how this can be fixed properly without removing the solar cells from the roof (an expensive task in and of itself), removing the roof cap, removing the Galvalume on that side of the roof, fixing the roof decking, installing the flues and new Galvalume in a coordinated fashion, then replacing the roof cap and the solar cells.

I’d really appreciate any suggestions or thoughts.