1. Can a Magus throw a melee weapon as part of spell combat? How about throw multiple melee weapons?
2. Does Rapid Shot apply to throwing weapons? Can you use spell combat and rapid shot?
3. Assuming he throws a weapon without a throwing distance, is the -4 penalty considered a non-proficiency penalty, or an improvised weapon penalty?
4. Can improvised weapons be enchanted, such as with the Arcane Pool Class Feature?
5. If he takes improvised weapon mastery and begins to throw glass bottles, do the glass bottles have a 19-20x2 critical range? If he does, would improved critical, keen, and other such effects further increase the threat range?
6. Finally, if a Myrmidarch has a 19-20 crit range with his weapon, rolls a 19, and confirms the critical while delivering a ranged touch attack spell (via "Ranged Spellstrike") will the spell also critically hit?
For 3 prior to the whole haste fiasco I would have said no you cannot rapid shot and spell combat. Now I have.no idea.
I can't answer on the throwing.
Pretty sure to receive a weapon enchantment an item has to be a weapon.
If you could enchant them the imp critical or keen would make it 17-20.
Ask how you would draw enough bottles etc with 1 hand to do any of this.
For the last one yes if you crit with ranged spell strike the spell would crit.
Rapid Shot is a Full round action. It leaves no room for anything other than a 5 foot adjustment.
When making a full-attack action with a ranged weapon...
Like many other abilities, it is not any action type in and of itself; it's a modifier to a full-attack action. Thus you can combine Rapid Shot with anything else that is also used as part of full attack action, and with one ability that is a full attack action.
Now, the question is whether or not Spell Combat qualifies.
To the original questions:
1. Well, according to the combat section, "Melee weapons are used for making melee attacks, though some of them can be thrown as well," so I don't see why you couldn't throw a weapon. The question becomes whether or not you could throw more than one. The FAQ says that when you use Spell Combat, you must make all your attacks with the light or one-handed weapon in your other hand - does that mean if you're holding a dagger, you must make it with that dagger, or can you make the attacks with any dagger? I don't think the RAW answers that; as a GM, I might allow it but restrict it to Myrmidarch, since the overall 'flavor' of the base Magus seems to be a melee combatant rather than a ranged one.
2. Spell Combat is a full-round action that is (now) treated as a full attack action for the purposes of Haste. It's not considered a full attack action for all purposes yet, such as fighting defensively. So again, no official answer on this yet. Again as a GM, I'd allow it for the Myrmidarch for sure.
3. As someone who feels that the improvised weapon rules can apply to weapons used an improvised fashion, I'd say it's a -4 improvised weapon penalty.
4. As written, the Arcane Pool class feature simply refers to the Magus's weapon. I would allow him to enhance unarmed strikes, natural weapons, and improvised weapons, since they are all weapons (even if they are not manufactured weapons). You'd still be restricted to only having one weapon enhanced at a time, and since using this ability is a swift action you'd only be able to enhance one dagger or improvised weapon - so it'd better have returning on it.
5. Yes, and yes.