Farming better, all the tips I've ever seen are that it just takes practice. Start up a custom game and shoot to get as high as you can with a particular champion.
Trading better in lane is tricky, obviously you have a whole laundry-list of things to avoid such as overextending, not having vision, and taking free damage from minions. Obviously, especially if it's early, harassing/trading with an enemy as soon as waves clash and they come in to cs COULD be considered a smart trade, particularly if your abilities can eliminate the enemy minions in the course of harassing the opponent. Free damage on them is good, free damage on you is bad.
One thing I've found personally, and you may already know this but I'll mention it anyway, is that mid is probably the most ganked/harassed lane by junglers. It makes a certain amount of sense of course, but it's still an adjustment to bottom or top lane or even jungling, where things have a slightly greater degree of....'safety' I suppose.
The other thing I've found, again that I'm sure you know, is that because of the more gankable nature of mid-lane, it's important not to panic when you get jumped on. Say you're pushing Nidalee to her tower and you happen to spot rengar coming from a side-bush. Don't panic! Don't flash! Don't blow your ult! Just...walk. Start moving right away, but just move. I've found that staying calm and focused during ganks in mid-lane can mean the difference between getting away or even getting a kill, and dying or possibly losing a tower. Of course it's natural to panic a little if you see, say, four enemies come mid, and if you really are in a tight spot don't be stingy about blowing that flash if it saves your life, but keeping your calm seems to help.
It seems like you've got good goals and good ideas for when you've got a lead. The farming and trading practice should hopefully help you get that lead more consistently.
As far as shot-calling when you're behind, I'm still not sure on that one myself. There's things you can do when you personally are behind, but when your entire team is behind it tends to be difficult. One thing I USED to do back in season 3 was ward the living hell out of our side of the jungle. If the entire team has fallen behind then odds are outer turrets are down, which means the teams will usually invade your side of the jungle to steal buffs, farm, and hope to catch you and your allies out from an odd angle and capitalize on your reduced vision.
By falling back to a safer position and having consistent vision of your jungle, you can begin to play smarter and make picks in the jungle, hopefully winning small skirmishes, which lead into teamfights in your favor. It was easier for even a guy like me to do it back in S3 due to no ward limits, but these days it's more difficult to pull off since 3 wards and a pink can still leave pretty big spaces for your enemy to slip through undetected. Unless you can get the entire team to sacrifice some gold for wards, you're gonna have a rough time getting the coverage that you need.
You also need to do it at the right time, so everyone has enough time to gain some gold for a round or two of the things before you get starved out. Being behind against a good team without vision not only decreases your chances of survival, but it starves you out in terms of gold. It's just too dangerous to cs too far from a turret or base, and even the turret becomes less useful as enemies become strong enough to dive for extended periods of time.
