(1) All prices depend on your Mercantile and on how much you are liked by the trainer, trader, etc. Increasing Mercantile causes "deflation" in Morrowind: all prices go down but also you will sell at lower prices. The liking can be improved by bribing. The bribing has a permanent effect.
(2) The prices differ slightly. They depend on the trainer's (trader's, etc.) Mercantile skill. The higher is the skill , the higher are the prices.
(3) Skill: always one point. Attribute when levelling up: 1 - 5 points depending on how much you have improved skills with with have the attribute as the "leading attribute". It is unimportant which particular skills you have improved, only the sum is important. You need 10 points for "x5" multiplier. The improvements aren't random.
(4) ???
(5) If you eat an ingredient then only one effect of the ingredient is applied. It can be the right one, it can be the unwanted one. Most of ingredients has 4 effects.
(6), (7) Skeletons are bit tougher than rats and kwama foragers. Wait with the tombs a bit but you need not wait too long. The islands are the same as the mainland: some places are dangerous some are not
(8) Go into the water and move forward (not down). You will swim on the water level. If you get hit then you usually get underwater, well, move up, back to the water level.
(9) None.