1. If you are a merchant you can have 15 pets on your profile before you can't hatch anymore, for ranchers it's 25. You can open a showroom (click on the little doggy thing on the top left of the screen) to store as many as you want, just keep upgrading to store more.
2. Your food pen will automatically feed your pet to 70/100 at reset (midnight Res time), just don't put unlimited food items into it, they will disappear. The best thing to put in is pizza or apples (since you can get a free one with each Creatu every day at the apple tree)
3. Umm.... this is a hard one, the new inventory isn't showing how much each piece of food feeds. Just feed them until they're at least "not hungry" (so that or full or something) and you'll be completely fine.
3.1 Your Creatu will eat anything and it doesn't really matter what. The difference between food items is how many points of hunger they fill, that's all.
4. They do not die when they get old. They die when they have been at "dying" hunger status for I believe 10 days (maybe 15... I always get those flipped XD) For example, my oldest is over 1,500 days old and he's still growing, don't worry, they are immortal based on age.
5. 0/100 is "dying" and 100/100 is "full" (actually, I think 70/100 is full too but whatever) so the higher the better.
6. Healing Water can be found in the Pharmacy. You don't really need to do the resurrection quest unless you have a dead pet though :)
7. The flowers you find every day don't change throughout the day, but they do change at reset. They are different for each person. So just keep trying every day. The flowers the botanist quest man asks for change every day as well so having lots of different flowers is good too.
8. Items for all other quests can be found in NPC shops (found under the Shops menu). This excludes Kir's Quest, which is a quest for pets and is a very long and difficult quest. Anyone can do it and can complete it (you won't run out of time on a quest) but it's geared toward older players to give them something to do. It also gives newer players something to strive for.
9. The selected pet is the one that things happen to (like if you use an item that affects a pet, it is used on your selected one) so other than that, not really.
10. Swords and bows and other such items are weapons. They will be used for battling, which is currently under construction but will be up ASAP.
whew, I think that's all of the questions. If you have any others, feel free to ask. Before you ask though, a great place to answer questions is by going to the Help link to your left anywhere except the forums. It's a basic FAQ for you to read through :)