Don't be leery of cutting a ducting hole through asphalt shingles-- just use a hook blade in a utility knife to cut what you need out of the shingle(s) THEN use a hole saw to cut the roof deck. I have always used a jig or recip saw myself because I hate using large hole saws.
Lap the uphill shingle over the duct flashing, lap the downhill one underneath, and use sealant under the flashing, the uphill shingle at the cutout, and anywhere you might have pried that shingle loose from one underneath. Screw the flashing down with gasketed screws and that should do it. I seal around the screw heads also, because it's too easy to crush those little rubber gaskets.
That's how I do it.
'7? Benelli 650S, '80 BMW R100 RS, '07 KTM 990 Adventure