Do I Cut all the the stems of the buds when I am ready to put them in jars?

Even the tiny ones that are holding the buds?

I would only cut them at the base of each cola. I mean really it's all a matter of personal preference, but I wouldn't dig too deep into a bud as to cut it into shake. Use your better judgement. If they are dry enough for cure then they ought to look like they do if you were to buy them cured at a dispensary, except for maybe a few color changes. The basic shape of each nug should already be there though at this point.

get rid of as much stem possible

I cut everything off, even the small "sugar" leafs imbedded in the bud(use em for hash/butter). But I leave a nice 2 inch stem to hold onto so you're not touching the buds them selves. I also sell em this way to friends and they seem to really like it