installing chimney thru rolled roofing

I think I would cut a slit horizontally in the asphalt, and slide the flashing up under the slit. I would use a high quality neoprene caulk at the seams and junctions. BlackJack Neoprene is my preferred sealant.

Hopefully "Hogwildz" will be here shortly - he help me out about my rubber roof install last year.

hello proud alaskan...i installed a metalbestos and roofjack (of course) through rolled roofing this fall and haven't had any problems. used blackjack roof cement/patch. i had not tarred the seams of the rolled roofing when i originally installed it, so i was able to pull the nails and roll the roofing away from the desired location. i did have to cut the roofing vertically at the point of the penetration and then i used a leftover piece of roofing to overlap the seams of the cut. i also used the roof patch to go over all of the nails i had pulled. this was done during warmer weather so the roofing was still a bit pliable. (50f if i remember). if you have some warmer weather coming your way (above freezing) i'd say go for it and work gradually. i used a flat bar to help peel the roofing. i hope this has helped and good luck, from a proud yooper, eh??!!

I had a miserable time with mine. Freeze thaw cycles always won until I put trusses on top of the flat roof. I would build a box on top of the roof, flash it and then go through that.

How much pitch do you have to work with? My problem was we get enough snow that it built up, froze/thawed a few times and eventually ice dammed a lake around the chimney. It didn't matter what I did to layer the materials, it eventually failed. If you have enough pitch it might not be an issue for you. I ended up shoveling the roof until the trusses went up.

No offense, but roll roofing is the least desirable, and worst performing/lasting roof made.
It shrinks, cracks, weathers & deteriorates at a much more rapid pace than any other roofing.
That said, it is asphalt. Hence asphalt roof cement & fabric tape are what is made for this type of roofing.
As stated, freeze/thaw cycles are this roof's Archilles heel.
I see two choices:
As already stated, cut a horizontal slit in the roofing and slide the top of the base flange under and leave the bottom of the base flange over the roofing.
cement & tape all the nail heads and the slit. I would also put some roofing cement at the area the flange goes under the roof along the entire say couple inches worth of the roofing underside and base flange top side, sandwiched in between. And also put some of the cement on the underside of the base flange where it rests on top of the roll roofing.

The second method is cut your hole as needed for the pipe, then set the flashing base flange in roof cement over the entire area it rests over the roll roofing. Nail the flange, then cement & tape the entire flashing edge all the way around. Very similar to doing a drywall joint. But using roof cement & cloth tape. Keep in mind to keep your 2" to combustibles clearance.

If you ahve decent enough pitch, I would shingle that roof, lay some rubber on it, or do something, anything other than roll roofing. All that crap is worth is short time on a shed.