I am looking for advice regarding this metal roof installation. In particular the flashing detail(s) around plumbing vent stack and exposed fasteners with lack of sealant. Thank you 
Mark,
Is this a re-roof?
If so, the lazy installers may have utilized the older flashing on the underside. But I’d still call it out (as I do with new asphalt shingle installs with tar sealant applied to penetrations) as defective flashing.
Here’s a great link on metal roofing and flashing…
http://danperkinsroof.com/VentFlashings.pdf
This is a re-roof over skip sheathing (shake/shingle was installed before). The rubber membrane flashing at the butterfly roof structure doesn’t look good to me either.
The rubber termination is a hack job.
I’d write this entire roof installation up as… shoddy workmanship.
Tell me something…(we don’t have butterfly roofs here), what benefits are there in building a butterfly roof over a structure?
Yep, they built a little rubber dam at the bottom of the valley.
Butterfly roof= big, flat valley waiting to leak, eh?
Exposed fasteners without sealant are acceptable on some roofs, we see lots of them here, but the fasteners should be gasketed.
That vent needs specialized flashing which is typically sealed and screwed to the roof.
That pipe is the pits. Hip and ridge may be OK. Vents, look as if they could have been done differently. Not much detail there. Does the water empty into, or onto the roof there?
Thanks for the great document 
The underside of the vent penetration was limited due to lack of access.