I highly recommend OSI Quad caulk for sealant. As Oldman47 said if you can find a matching piece of roof tin slip it under the ridge cap and bring it down and over the top half of the roof flashing.
Getting another sheet of metal roofing to over lap the to half of the flashing is the easiest way to handle your install. They do make some fancy products specifically for metal roofs, just Google "chimney installation in metal roofs". Another consideration you should take is if you get a heavy ice load or about load it can damage your pipe if it slides down the roof. There are products you can buy to protect the pipe or you could try making your own.
that looks like a great idea marsy. Ill be looking into somthing like that. Got it all hooked up and burning today. Cut the hole on roof close and siliconed around it today with what the hardaware guy gave me. And thats not so great. Its already heated and running down the pipe in the attic. Im going to rethink the roof area tomorrow when i have more time. but the rest worked great.
I like the strait pipe vs. any pipe with any kind of bend in it. Every bend will slow down drafting and slow the burn time. Behind my shop stove is where I store lots of steel pipe, angle iron that can trap and hold heat, that will put out heat over time later when the fire burns down.
Instead o the normal thin walled stove pipe that most stoves use. I substituted it for a 1/4" x 6" galvanized steel pipe.
That pipe will never burn out or even rust out.
If you want to seal around your storm collar, use high temperature silicone. That is what it is made for.
Just an example from a quick google search. I do not endorse this particular brand because I have no experience with it. http://www.deaconindustries.com/?gclid=CPWNgq3QxcoCFQqtaQodZGUCog
made a nice angled rain deflector last night for the roof ahead of the chimney and we got a lot of rain last night and today. Cant wait to check when i get home. Hoping no leaks! Ill try to get some pics up.