Who fixes this?

I don't know the term for this, but I have a roof where two planes meet, and there is a metal trough that runs down the seem, for water drainage. Some brain made the exhaust pipe of the water heater run straight up, through the "attic" and up through the middle of the trough. I would like to have the pipe rerouted inside the attic and moved over so that it pops up through the roofing material instead of the trough. So, who would reroute the pipe, replace the trough (now with a hole in it), and deal with a new hole in the roof? Would a roofer do it all? A plumber? Both?
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An HVAC guy can move the vent over and make a new hole in the roof and flash it properly.
A roofer can fix the valley flashing, possibly by putting a new piece on top of the old if the hole is close enough to the top of the ridge. If the valley flashing has to be replaced, it's a lot of labor removing shingles to get at it, will probably cost many bucks.
Even though this is poor craftsmanship, if this setup isn't leaking, I wouldn't monkey with it until you have to replace the roof anyway. At that point it would be easy to fix properly.
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wrote:

Good call MarkL.
To that I would add, even if there is a minor leak it might be better to patch it and limp along until you need the roof. If this is located on the upper end of the valley there may not be a lot of water flowing at that point. The proper repair is a big project.
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It was leaking last night. We had a torrential rain, and there was a small stream of water flowing on the outside of the exhaust pipe, from the ceiling to the water heater.
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What kind of goop do I use to reseal around the pipe? I'll wait until things dry out before I do it. By the way, I've never seen leaking before until the big rain last night. The pipe is midway down the valley, unfortunately not at the top.
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Some links you may find helpful...
http://home.howstuffworks.com/how-to-repair-a-leaky-roof2.htm http://home.howstuffworks.com/how-to-repair-a-leaky-roof3.htm
Don't talk about the abomination you have of the vent through the valley, but show how each is dealt with individually.
Not able to see what you actually have, have a few suggestions -- first, if there isn't a flashing collar around the vent, if the the valley is wide enough you might see if you could manage to take one of the right size and modify its base to fit the valley and set it in w/ roofing cement. If the crease is too sharp that may not be feasible.
Alternatively, my other idea would be to use some of the flexible sticky-backed rubber membrane and fit it around the joint. It is flexible enough that should be able to make a seal.
If it's a real abomination, might be well worth the effort/expense of getting a roofer to move it. Depending on the location of the valley and what is in the attic, etc., may be able to move it only a couple of feet and simply put an offset in the pipe in the attic. That's a pretty simple operation. If there's an obstruction like a brick wall or something that's the cause of the present location, that's something else again, obviously.
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