Glad they're (mostly) back together.
FWIW, I just thread all fasteners hand tight back into the holes they belong in. That way they don't get lost. The only parts that are separated during shipping are the pedals and QR spindles, which go in a little nylon zip bag. "Ton of tape" gets reserved for the RD, which I remove from the frame but *not* from the chain or cable, so it takes a lot of tape and foam to keep it from rattling around and scratching the chainstays. Removing the chain for shipping would be more elegant, but I don't bother with that unless I plan to replace it on arrival.
As far as handlebar placement, what I do is put a tiny dot on the handlebars with a Sharpie on each side of the clamp. It's barely visible once everything is back together. Piece of electrical tape to mark the seatpost height, unless there are markings already on the post that I've recorded.