Proper installation for furnace flue Pictures please

I have a nightmare of a roof installation. It is an r panel roof with the rib 1.25 inches tall. This is residential.
I need to see pictures and layout of how and WHAT to install for the flue and to a lesser extent the plumbing vents. I have the silicone roof jacks but I don't know what goes above that. I would think there has to be some kind of a lid/top on that.
The roof has skip sheathing with Deck Armour and storm guard around the perimeter. On top of that, we installed 1x4 batons, running horizontally every 3 ft. Then we have r-11 insulation with a vapor barrier. The longest run of the metal panel is 18ft.
I asked my inspector at the progress inspection what to use and he said use mfg. specifications. The panels were made by Nucor Steel. I can't find anything online and not much help when I called them either.
I also need to know what the valley metal supposed to be per mfg specifications.
I dismissed the installers because nothing was done right. The valley end cuts are all over, they didn't screw down the panels in many places. Some of the holes for the penetrations are so big that the boot didn't cover so I have purchased new boots. There are raw edges on the rake trim etc.
Thank you very much for taking your time and helping me. I am trying not to have to take apart the entire roof.