1. In order to use Spell Combat, you must have a hand free. If you're busy drawing an Extract vial both your hands would be occupied - so I'd say no, you could not (assuming that the "must be on the Magus spell list" literally means as long as it's on the class's list, and not being cast from one of the class's spell slots).
2. You would need at least 4 arms, because Spell Combat requires that one hand be wielding a light or one-handed melee weapon while the other hand is free. Hands 1 and 2 would be wielding the two-handed weapon; hand 3 would have a light weapon; hand 4 would be empty.
3. My understanding of Spell Combat is that your free hand must start free and remain free for the duration of the action - so no, I don't believe that would be allowed.
Since what it seems like you're shooting for here is delivering spells via Spellstrike using a two-handed weapon: As far as I'm aware the only legal method of doing so is to burn one round casting the touch spell, holding the charge, and then the next round delivering it via the two-handed weapon.
2: If you take a Vestigial Arm can that arm being free allow Spell combat while using a Two-handed Weapon.
Per the FAQ (http://paizo.com/paizo/faq/v5748nruor1fz#v5748eaic9qhf), you can only use a light or one-handed melee weapon, with spell combat, and can not attack with additional limbs or attacks. So the other two arms won't help you in spell combat, except maybe giving you a choice of which weapin to attack with.
If you allow 3rd party products, the "Advanced Feats - Might of the Magus" books has feats that allow two-handed spell combat. The book is nicely balanced for a third-party product, I'd say, but your DM has to allow it, it is not core Pathfinder.