"Sweetchuck"
"a) Later in the game, a lot of my cities start tanking on granery stock and I get big, red "SHORTAGE" tags on my city pages. What causes this and how can I remedy it?"
You irrigate or rail tile tha are irrigated to get more food, but at some point you will max out food. You have to try to get the town so that it produces food that is divisiable by 2 or you will end up with shortages.
"b) Also later in the game, I notice that many of my larger cities (pop. 22 or so) start disordering civally because of "100% - it's way too crowded". Even if I have a bazillion workers working the tiles and all the tiles in the immediate area are improved. but, say if the surrounding tiles just outside of the populated boarder (the boarder within the city limit boarder) are, say jungle - does clearing that outside layer of jungle improve this?"
Disorderly is best handled by increasing lux or happiness improvements. After you have more than 21 pop it should be fine as all other pop will be specialist and that tends to help.
Jungle not in the borders will not affect the citizens.
"c) Can you automate certain workers to do one thing (like build railroads around towns) and certain other workers to do some other thing (like clear jungle or irrigate)?"
Yes, but I do not do it. Never trust the AI to manage anything. Ok, if you own the landmass, you can automate cleanup.