1. I've noticed my science officer wants less pay than my navigation officer despite having higher skill. I'm guessing this is because I acquired him at a high skill level and my nav officer at a low skill level. Is it cheaper in the long run to hold out for someone higher skilled?
Can't answer that I'm afraid, I have had no crew ever. They fart in their space suits and make too much noise. And besides, they far in their space suits.
2. I seem to be most unpopular with the rebels and the guild. I've noticed that all their missions require combat. Is this axiomatic? Is my quest as a civilian likely to mean these are always the factions who hate me most?
Don't count on it. You will find yourself in systems where the Rebels and Guild ships like you more than the Navy.
3. I've been working on upping my reputation in Olympus and Cerulean. Does this degrade when I'm offline?
I could be wrong here, but I think you need to bring the reputation up to a full 100% for it to stick. If you don't and you log off beforehand, your reputation will drop again to its previous level due to your 'lack of commitment' towards those factions.
4. After completing a couple of contracts at any given station I tend to run into six hostiles from the other factions lying in wait for me. Is this normal? The more missions I complete for one faction the more enemy ships I will find waiting to ambush me? (If so I guess the best plan is to do a couple of missions then move on.)
When you are hostile to a certain faction, they will communicate your position to a nearby base, which will then dispatch more ships to intercept and engage you. I'm not sure whether the numbers change in relationship to your level of hostility towards that faction, but it wouldn't surprise me.
5. What's some good weaponry to have? There seems very little info available on them other than the three stats which I'm guessing are Yield, Cooldown and Range? What's a good particle/beam combo?
The 'C' stands for 'Cycle' (refire rate) rather than Cooldown. But I guess it comes down to the same thing.
You will find that most experienced players prefer to use a low-level combination because of the lower energy drain and the resulting sustainability in fire power. Low level weapons, which consume less energy, will keep firing, even if you are hit by enemy fire and your power reserve is empty. The higher level weapons simply consume too much energy to still be able to fire when your energy is empty.
6. Fulcrum jumps use my weapons' energy bar. I can shift power to weapons to decrease the wait between jumps. Is there another factor I can use to minimize the waiting period? IE: something to buy which reduces the time taken to recharge weapons.
The only thing I can think of is buying a higher level ship, or a military frame. Both offer a larger energy reserve, and I'm betting a faster recharging cycle.
7. When I'm hiring crew, I also see some ships looking for crew members to 'board' them. How does this work? Are there any benefits?
Seeing that this concerns crew, I have no idea. I do know that they far in their space suits, though.
8. I see recently that below my kill count it also states "Fleet: 0". What's this? Does it mean I can hire AI fighters as wingmen? How do I do this? How many can I have? What happens if one gets shot down? Will they fire on any hostile or only someone I myself have fired upon?
Yes, you can hire ships to be part of your private fleet. You do need to be fully friendly with them in order to be able to do so though. You can give a variety of orders to the ships in your fleet. Can't answer the other questions, never tried hiring a fleet.
9. Can I own more than one ship? IE: 1 civ 1 fighter, so I can switch between them as the mission requires.
Yes. Firstly, you can have as many accounts as you want, each containing a unique ship and setup. You can switch between accounts to change ships. Apart from that, you can also store your ship inside a stations hangar. This will cost you money each time a system cycle completes. I believe the price is around 540.000 per cycle. In order to do this, you click on 'Enter Station' when you are docked, then click on 'Hangar' on the bottom left. You can now store items from your ship into the station hangar, or even your ship itself. you can then buy another ship, and when you are ready to switch back, you click the 'Swap' button in the middle of the Hangar interface. This will swap the stored ship for the one you are flying at that time. So if you combine the fact that you can use numerous accounts with the notion that you can store ships in hangars, the options are literally endless.
10. Can I store goods to retrieve later? How do I do this? Are my stored goods only available from the station I put them in or from any station? If the former, how do I track which stations I have stored cargo in?
Yes, see point 10. Like your ship and equipment, you can transfer anything from your cargo bay to the station hangar. They are only available in the station where you left them. To answer the last question: I don't know, how do you keep track of the spot you parked your car in? You remember.

But seriously, if you have trouble remembering, just wright it down somewhere, or add the station location to your map log.
11. What does an afterburner drive do?
It uses power from your ship's energy reserve to temporarily increase the output of your standard afterburner. This results in greater acceleration. Beware though, the effect only lasts while your ship has energy and the energy needs to recharge in order to use the drive again. And when you're power's down, you cannot jump either.
12. Can two or more indy pilots share a contract or is it clan only? How?
Yes. Contract rewards (ie credits and rank/rating increase) are extended to any pilot who flies in the same sector as the pilot who took the contract, regardless of it being a military or civilian contract, or the players being clan members or not. As said, this works automatically, you do not have to click any buttons. The reward is not shared among the players; each player receives the same reward.
13. Can indys build stuff? Does this affect clan control?
Yes, works the same way for everyone. Just buy a Build Constructor and start building. As long as you don't use another clan's clan tag, your stations will not interfere with other clan stats. You can however, get permission of a clan to temporarily use their clan tag and build stations on their behalf, if you for example want to help them out.
Doing contracts from a clan tagged station only affects the clan percentage in that system if the player doing the contracts is tagged with the correct clan tag.
14. On the left HUD, what is N, W and S?
N=Navigation, W=Weapons, S is a misspelling, it's actually an E and stands for Engine.
(I am using another cockpit than the default one, so it could be that you are correct and it is an S and not an E, in which case I would assume the S stands for system).
15. What are wings for?
They increase the surface of the ship so enemies can hit you more easily and you have to pay double because you need two parking spaces.

Just kidding. Stability, maneuverability and agility, I'm guessing especially in atmospheric conditions.
16. Where does one acquire gold and/or silver?
No idea, I don't mine.
Hope that helped.