1) Although I myself do not do this, the best thing to do would have all the villagers build a farm, making them walk towards the farming area. Then select one villager out of the whole bunch and have him lay down the rest of the farms. And then, if possible, task each individual villager to a different farm.
If you feel this requires too much work, you can just have all the villagers lay down the farm foundations, and then just let them sort the rest out themselves.
Don't shift-click.
2) I only have this problem when the farm my gather point is on is not close to any vacant farms. Just reset the gather point when all close farms are being used.
3) Don't have wood/gold villagers (or food) gather at the same place as this is unefficient. Because there are so many villagers, they will constantly be getting in each other's way. Try to keep less than 10 villagers using the same dropoff site.
4) This is the most difficult question to answer, as it always depends on the map, and how the game is going. First off, some basic economical advice:
Don't feel that you have to go from hunting to hunting. Also, don't have all your food gatherers at the same place. When you have, for example, a situation like this...
(hunt) (berries) (hunt)
don't go straight from the hunt to the hunt. Since berries are in the middle, gather from them. You'll use that second hunting patch anyways, and it will add un-needed walking time if you skip the berries the first time, and then move to them once the second hunting patch is depleted.
Another thing to consider is map control; don't hunt in an area that can be raided easily. If there's alot of hunting, but it's all far away, don't hunt from it. (like Marsh; lots of hunting but it isn't wise to hunt all throughout classical age) Another thing to consider, is that once a villager has begun farming, it won't ever stop. This isn't true about hunting; you may be good at keeping villagers busy, but say you're in the middle of a battle. You're microing your army, creating units at your buildings, etc... what happens if your hunting villagers become idle? First off, you probably won't even notice, and even if you do, you normally can't afford to re-task them, as this will lead to a neglected army.
The problem with most lower-rated players is that they don't make good decisions about archaic/classical food dilemmas.
5) Regardless of whether you win or lose the water, fishing is advantageous. However, once the game reaches Mythic (maybe heroic) fully upgraded fishing is slower than fully upgraded farming. You may want to slowly switch to farms as the game progresses, but don't worry too much, farming is only a little faster than fishing.