Best way to attach metal flashing to rubber roof?

I commend you on the Oslo, I'm a big fan. I'd probably take mine with me too if I should ever move.
As far as your issue with rubber roofing, I have some experience with it., being in the construction industry.
Your thoughts are all in the right direction although I would change some things. Since it's very difficult
to get under the rubber roofing as is, I would mount the flashing (exit boot) on top of the rubber roof using some
'black jack' cement/adhesive/chaulk. After cutting your exit hole (as tight as possible), and
continuing with rubber repairs, I would make the patch repairs with rubber cleaner and then rubber roof cement
along with the rubber patches around the boot, using wide repair patches to ensure a tight seal.

Silicone doesnt adhere. Black Jack cracks in a year.For modified rubber(torch down) use roof cment and fabric. For EPDM,use Firestone rubber caulk.

Be real careful with what you put on EPDM, many products will attack the EPDM reducing its life and voiding any guarantee. I once looked at a commerical roof that had been "repaired" with a tar based sealant. The EPDM was fine excpt where the sealing had been done, less than a year later from the "repair" the only option was rip it up and replace it.

If the new membrane is EPDM, I would most likely use 3 items to anchor the flashing for the flue pipe: Eternabond RoofSeal Micro Sealant Tape; Eternabond Double Stick Tape, Product Id: DS-1-50; and 5 appropriately size roofing nails. Clean the membrane with a quality primer/cleaner, use Eternabond Double Stick Tape between the roof and the flashing, place 3 nails across the top, one each in downside corners, cover edges and nails with Eternabond RoofSeal Micro Tape. Eternabond is much like bar anchor tape that Pen mentioned. Care must be taken when using it - once it's placed, it's not coming back up - period. The stuff is not cheap, but it works and I hate redo's. I've never seen Eternabond in big-box stores and for small quantities it can be found cheaper from a place called RVUpgrades.com (I am not associated with them in any manner) For larger quantities, there are several commercial suppliers.

Just got your PM, and replied back.
If it is truly a Rubber / EPDM roof:
Blackjack or any asphalt based caulks & sealants= NO GOOD, will eat the rubber.
Silicone = NO GOOD won't stay stuck worth a damn or for very long.
Put the flashing over the roofing membrane, with "water cut off mastic" bead underneath the roof side flange. 1 bead 1" around the center hole opening, another brad 1" from the entire perimeter. set on the rubber in place, screw the roof flange tight by reaching the decking with screws. Flash with uncured EPDM, and lap seal all the edges, seams and overlapping joints.
The water cut off & lap sealant comes in regular caulk tube form.
The uncured should cover minimum 3" of the roof and continue onto the metal flashing base and wrap 1/2" up the vertical portion of the roof flashing. This is easiest achieved in 2 pcs overlapping each other.
Then a single pc wrapped around the vertical part of the flashing and wrapping 1" down onto the rop of the previously installed roof part of the flashing. See attached diagram.
If you have any questions, PM me.

http://www.carlisle-syntec.com/documents/ResLib/07_U14A.pdf

^^^He is the man when it comes to flashing. I was fortunate, Hogwildz only lives a few hours from me and he came and gave me hand with my EPDM roof/flashing.

Archer39 said:

^^^He is the man when it comes to flashing. I was fortunate, Hogwildz only lives a few hours from me and he came and gave me hand with my EPDM roof/flashing.

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How did that stove work out for you last winter?
Everything holding up well?
Did you figure a way to get the heat through the house?