Welcome to the game, hope you'll stick around,
2. Does anyone bother running homes?
Compare those 8 peasants (and the removal of 25 jobs, which is a very good thing) with the effects of other buildings. In some situations they're a decent choice, especially for conflicts due to the birth rate bonus.

4. What is the maximum % bonus for all sciences?
5. What does the bonus modifier under each science area mean in the guide?
bonus = modifier * bpa^0.5
Where bpa = books per acre. As you can see from the above, there is no max as it's a square root function.
6. Is there a general defense per acre guide for new players that tells what general defense to run each day?
The first 2-3 weeks of the round are very hectic, with way lower military ratios than later on. How much defense to run is a heavily debated issue. In conflicts, you should line up with your kingdom somewhat. It's no use to have 75 DPA if your kingdom is running 45 DPA, same if you run 35 while they have 50. Many newbies run too much defense in a futile effort to stay safe. While defense may sometimes keep your province safe, offense helps keep your kingdom safe.
9. Whats the highest land you can safely leave protection on and still be safe, assuming you start at the beginning of the round and are playing a fast human with all specs?
Not a newbie question, hard to answer. The problem is that the safety of your province depends to a large extent on how much backup your kingdom can give you. For the most part, any top 100 province in a kingdom that isn't top 50 (probably top 20, rather) will get chopped up and eaten first 2-3 weeks. If you're only planning on racing up during protection and first 2 days then pump and drop, that may work better. You'd generally be better advised to grow in moderation without a strong kingdom to back you. Explore to maybe 700-800 acres during protection.
10. Would a top land explorer need to raise his draft rate higher than the starting rate to reach top land and still be able to defend himself?
A word on draft rates first. If you're active (minimum 2 logins per day, average 3-4) and playing in a somewhat organized kingdom (not necessarily top), you should always be at 80% draft rate. Instead, vary your draft with the speed setting. If you produce too many soldiers, lower to reservist and send what extra you have to others in your kingdom. That's far more economical than being self supplying and having to run Normal sometimes to get enough soldiers when demand is higher.

For a large explorer during protection, you'll probably need to draft from the start. Again, don't think in terms of the draft%. Think in terms of drafting or not, and at what speed.
11. I read somewhere that mills where not described properly in the scribes and you can't get free exploration costs. Can someone please explain exactly what mills do?
They are properly described, but the building effect isn't proportional with the building%. If you have 30% of something, you don't get an effect of 30% * modifier. Instead, you get 30% * (100% - 30%) * modifier = 21% * modifier. That's called diminishing returns on buildings, promoting diversity in setups. Max effect you can reach is 25 * modifier (mills modifier is -3 so max effect is -75%).
13. If I play by myself as an explorer will I have to run lots of mages/spies to stop people from raping me in a war or will I be ignored since explorers are less of a threat?
If you play as an explorer without offense, thieves or wizards you'll be completely useless to your kingdom in any conflict and be taken out very easily. Playing as a T/M (thief/mage) can be a viable choice, but I advise against it. If you wish to learn the game, playing attacker is the best way. You're too sheltered as a T/M and often not enough use to your kingdom.

14. Whats the fastest possible return time an army can have?
List of factors:
base time = 16
Learn/Plunder/Massacre = *0.875 (war room displays this wrong)
Ambush = *0.75 (ditto)
Quick Feet = *0.9
Aggressive = *0.9
Warrior = *0.85
On-island (if not at war) = *0.9
War = *0.85

Note that the bonuses are compounded. Hope that helped!