1. For the actual math you should probably look at the code, since it gets a bit involved. Basically the player makes a skill roll, the opponent makes a skill roll, and whoever's roll was higher wins.
2. No. The penalty only applies while travelling at full speed.
3. I thought this bug was fixed a while back? Lemme check... Yes, this bug has been fixed for both GH1 and GH2.
4. No, with the exception that flying mecha are usually so high they can't take advantage of cover.
5. No, no, and no. See TheRules.txt for details on what parts can incorporate what other parts.
6. The wiki page says that? There are certain cases in which a problem can be solved by multiple skills, i.e. Science and Investigation, or Investigation and Code Breaking, but Science cannot generally be substituted for anything else.
7. No. All melee weapons are capable of scoring multiple hits, depending on the skill level of the attacker.
8. Magazine is the maximum number of shots that the weapon can hold.
9. As long as you have unspent MP, instead of taking cyberdisfunction points you will lose MP and morale instead. This means you will gain disfunctions at a much slower rate, but will spend much of your time exhausted and angry.