I realize that all of the concerns you posted were of a more technical nature and I can't help with that.
But follow up on their references, that's all.
I did a major roof replacement last year (went from shingle to metal) and it was a wonderful experience from the beginning. But I chose my contractor by talking to folks they had worked for as much as by how they struck me themselves or what they promised to do.

Around here finding someone who actually returns calls is half the battle :)
Good luck!

felt is installed to shed water. first layer goes
on at eaves and is installed overlapping runs to
peak of roof.any decking would be replaced as needed
prior to new felt.

valley flashing should be reusable.
if not replace what you have to.
it is only when it is exposed that
this call can be made.
if they use care in removal...they should
be fine if no problems previously.

keep in mind..if it matters to you
that the new copper will be shinny as
opposed to older weathered copper.
in a few years..it will be about the
same.
this would't bother me..but some folks
it would drive nuts. go figure.

as shingles/shakes go over valley flashings
I don't see how thickness of shingle would
effect anything.
I've never worked with shake, but with slate
to shingle nothing changed flashing.

replacement of venting requires proper flashing.
question them about how they plan to flash these
areas. I prefer a rubberized roof boot as it makes
a tight seal around vent pipe. this boot goes
under the shingle at the top of the vent. nailed
under the shingle lap. sides of the boot are under
shingles...but bottom of boot is on top of
shingles. so that any water that may enter has
exit point.

replace the drip edge. cheap product
that won't add much cost to the job.
drip edges get damaged easily, so replacing
them wouldn't be an issue for me.
(felt over drip edge..make sure this happens)

on your own..check what wind zone requirements
are and make sure that shingle is rated for
that zone. also find out how many nails per
shingle and make sure that the correct amount
is used per shingle.(that may be a hurricane
zone thing...not real sure) but info for your
area wouldn't be difficult to come by.

do you have any venting or leaks in your roof now?
any in the past?
what if during the tear off of shakes soft spots
(roof rot) is found? ask what provision is inclueded
for things hidden until job is ongoing.

personally we always walked every inch of the existing
roof checking for soft spots. inspected around
venting, chimenys & valleys.went into attic
to inspect back side of decking.
even with that..there sometimes were things that didn't
show up until exposed.
other things like facia boards should be inspected also.
I'd want to replace & prime any facia before roof tear off,
although paint could wait until warmer weather.

what about clean up & disposal of shakes &
waste from install? bits of new shingles, felt trimmings
ect will be around the edges of the house.
who cleans up & gets rid of shakes?

these are the things that come to mind.
I'm sure they will have enough sense to have
delivery of shingles to newly felted roof
by boom truck. this will eliminate the need
to haul shingle packs up the roof.
truck will distribute shingle packages, workers
move then to areas as needed.

roofing in the spring early summer is a nice job.
in the dead of winter or heat of summer...its
hard. keep bathroom or portapotty on site.
and offer coffee or hot chocolate on breaks.

where are you located?

best of luck.