Ceiling – Vaulting ceiling and removing ceiling joists without risking the integrity of the roof system

I would clean out the area around the holes to give myself room to work without being showered with cellulose. Open the holes a little: make them square, and big enough to be able to get your hands through. Next, get myself a roll of R-13 fiberglass batting (currently less than $10 at Lowe's or HD), and cut patches to fill the void in the cellulose insulation: you'd probably need two or three layers, depending on what size your ceiling joists are. Stuff them through the holes and spread them out. Finally, use a couple of 1x2's to cross each of the holes, and patch them as described in this answer to this question.

I've used a shop-vac for cleaning up blown cellulose, but for disposal, not for later re-installation. It seems to me that it has a very different texture before and after: clumpy and with some structure, versus powdery, no texture.

Go ahead and place the drywall over the top edge of the crown moulding. Sounds like the wall was already re-plastered with it in place. If you tried to remove it, you may end up re-doing the walls as well. Even forgetting that, it's almost impossible to remove moulding without sustaining some loss. Without replacement material available, removal with intents of preservation is extremely risky, especially with stain grade material. You don't want to go there.

If your joists were flat, you'd still only need to shim down the first 4 feet or so along the walls, no one will see the resulting slight slope. Keep this in mind when planning your shims. It doesn't have to be perfectly flat, unless that gives you pleasure. You also don't need to shim to completely fill the gap. An 1/8" gap makes a clean shadow line that is not detrimental (assuming it is perfectly uniform) at all. It also makes finishing easier. The taped joints of drywall are normally not perfectly flat, despite the tapered edges. There is a slight bulge which is usually invisible. But against straight moulding, depending on the profile, this bulge may be visible. You might consider grinding down the edge tapers at the board corners against the wall so the joint tape can be completely buried and the yet the joint against the moulding can still be perfectly flat.