You should have a wall thimble that allows the pipe to pass through the wall. The thimble should have a plate on the inside and outside of the wall and there should be a framed opening in the wall that the pipe passes through and the thimble attaches to. In most cases, combustibles are not permissible within the space between the framed opening and the pipe that passes through the thimble. I would not place anything in this space. It is possible that your pipe is a zero clearance pipe and therefore may be able to be in contact with combustibles, but I would not bet on it. If you do not have a thimble, you might want to have a contractor that specializes in stove installations take a look at it and tell you what type and size of thimble you will need.
Okay now I understand. If your pipe is double walled then there is usually a 6-8" clearance to combustibles requirement. This is imposed by the manufacturer of the pipe and so I am just speaking from the pipes which I have seen in the past. That said you may want to extend the pipe further from the wall or determine the specific manufacturer and get their requirement. As for the staples and the Tyvek, I would use plastic cap nails that are long enough to penetrate your sheeting and go into the studs since you are going to wait until spring to put the siding on. If you were going to put the siding on immediately then staples would suffice. You will also want to make sure the Tyvek is good and tight. Once the wind starts whiping it around, it will eventually tear off of the wall regardless of how well you nail it.
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Extensive experience in carpentry, plumbing, electrical and all other aspects of construction.