I also do the vast bulk of the material removal with a fingernail ground bowl gouge (though the 3/8" is my favourite). I get all the basic shape with the gouge and then finesse the corners with the scraper. If I'm bored I'll sometimes do the initial corner creation with the long point of the skew because the sheering action leaves a lovely finish on the end grain. But I always find the scraper is the easiest tool to finesse the final shape with because I'm looking at the top of the apple rather than the end of the tool.
For the 3mm stem, have you got a 1/4" detail spindle gouge? If you sharpen a small detail spindle gouge just before the finishing cuts it's absolutely superb at peeling away those last few layers of very fine material to get the thin diameter you want.