I assume you are referring to a ceramic tile floor (as clearly, the cabinets will have to be in place before you can install a ceramic tile countertop...:-). As long as the ceramic tile floor will not raise the level of the floor to the point that your toe space will be less than 3", then I would suggest installing it last. This will lessen the likelyhood that you will drop something heavy on your new tiles and break them.
You are wise to consider a softened ceiling from prior water damage prior to painting. I'd probe it a bit with a screwdriver to make sure the ceiling is still solidly attached. Its much easier to do repairs now than waiting until you've gone through the trouble of applying new paint. Also, the key to a good paint job on a textured ceiling is making sure the old surface is squeaky clean and dry prior to applying the new paint. A 50% solution of TSP and a good bristle brush is a good combination.
Code usually requires a minimum crawl space height of 18", although I've seen them with much less :-( I would re-install all insulation and hold it up with long wood strips (you can rip them from 2X4's (about 1/2" thick) if you have a table saw). Yes, you should put down at least a 4 mil plastic vapor barrier, and yes, I would make sure you have ventillation, while insulating ducts and exposed plumbing pipes.