More clarification:

I was a cabinetmaker for 4 years. Woodworking become a hobby of mine
and I've helped friends do some residential framing, but by no means am
I a seasoned builder or contractor.

I'm wondering if there's a specific line past which permits are best.
I'll be using a dumpster in the street for demolition so that's pretty
much a given permit situation. I have talked to the engineer about
vaulting the ceiling so I would anticipate being able to demo the attic
without affecting the ceiling joists. I do not have trusses to worry
about. I may install wider (2x8?) rafters to allow for adequate
insulation, venting, etc. And then if I decide to replace or move the
ceiling joists, I'm borderline in over my head and will probably need
to rely on some help.

The main point being that it will be taking me a lot longer to get
everything done, but both my girlfriend and I are prepared for this
(stepping over a pile of stock to get to the kitchen to eat breakfast,
etc.) But if I get permits for everything, then I will be under
pressure with time and this is something I'd rather avoid if possible.
To be sure, I have no intention of jeopardizing the safety of the
building. But the road to hell is paved with good intentions and
that's really why I'm asking here. I also realize the importance of
maintaining a decent relationship with building inspectors and I'm also
wondering if tackling some of this stuff without permits gets me off on
the wrong foot. I'm planning to run a lot of this by the inspection
department before I get too involved, but I figure here is not a bad
place to start.