Ok, here goes!
I'm only going to give an answer for the more commonly asked questions.
2. Are transported units considered to be in specific transporting units of their formation?
Yes. It's really important to keep track of exactly where you transported troops are. It's hard enough to kill Fearless Commissars but when they miraculously always happen to be in the last Chimera, it can get a little tiring. It may be more work for the player but it's the only fair way to play this.
3. When disembarking, are transported units placed completely within 5cm of the transport unit or just so one part of the transported unit is within 5cm of the transport unit?
As far as I'm aware, it is only in parts of North America that the entire base of disembarking troops needs to be completely with 5cm. There are situations where it would be all but impossible to be completely within 5cm (Ork Landers, Krieg Gorgon etc). The wording for disembarking (within 5cm) is the same as that used for the Commander special rule (within 5cm). The North Americans play it their way because they consider it an unfair advantage to the long thin bases (over the square bases). The advantage is real but small so it has generally been considered unimportant.
4. When does a unit count as being in cover?
Infantry are considered in cover if any part of the base is overlapping the terrain (or in base contact if agreed with your opponent beforehand). AV/WE's are considered in contact if they have taken a Dangerous Terrain Test or are actually overlapping the terrain feature (WE's in a river for example).
5. How many units can claim cover from a armoured vehicle, war engine, or terrain feature?
As Matt mentioned, it's generally considered to be 2 units per DC. So it would be 6 in base contact with a Warhound. 2 in base contact with a Chimera etc. Terrain is different. It's basically as many as you can fit (with the exception of fortified positions which have specific rules attached to them).
6. Does the charging formation need to get within 15cm of the original target or can it get within 15cm of any intermingled formation?
As per the rules, an attacker declares a target formation first and then declares any intermingled formations as part of the engagment. We have always played that the charging formation needs to get within 15cm of the original target.
7. How are attacks with special abilities like ignore cover and lance allocated in an assault?
In the absence of detailed rules for these abilities, I believe that the example of MW/TK attacks should be followed. i.e. these attacks should be resolved after normal attacks.
8. Is it possible to air assault into a formation which is completely covered by the zone of control of another formation?
Yes. The rules actually do allow this but the UK Epic scene has disallowed it. As far as I'm aware, they are generally the only group that has disallowed it.
9. Where should measurements for capturing/contesting an objective be made from?
General convention is to the centre of the take and hold objectives and to the board edge (middle) of the blitz objectives.
10. What house rules do you normally play with?
Things like CAPing enemy CAP is a house rule and generally not played here.
12. What is your army capable of (units, weapons and special rules)?
This is to try and prevent those gotcha moments when a special rule over-rides the rules (think Necron Living Metal which nerfs TK attacks and the Space Wolves Pack Mentality rule which is REALLY horrible to forget! ).
Hope that all helps.
For background on my answers, I am the NetEA Rules chair which means I compile/edit/amend the FAQ for the NetEA group.
This doesn't mean I'm always right but it does mean I've read the rules cover to cover and I have an appointed group of experienced players (from all over the world) to help keep the FAQ up to date.