Just a note on your sealant, I used to do the same around a roof vent like that, but after the second application of sealant it eventually built up a small ridge or berm trapping water between the vent and the sealant. After a heavy rain I climbed up to check my work and noticed that it was like a little mote!! Since then I use a wooden dowel to create an indentation at the corners to allow water to drain out and not sit up there..
I eventually scraped the heavy bead of sealant off and used Eternabond Tape around my vents and joints.
