1) "When you attempt to perform a combat maneuver, make an attack roll and add your CMB in place of your normal attack bonus. Add any bonuses you currently have on attack rolls due to spells, feats, and other effects. These bonuses must be applicable to the weapon or attack used to perform the maneuver." Anything you add to your weapon attack, you add to the maneuver, so Weapon Focus and magical enhancements are added. Tripping bonuses from the feats and the weapon itself all stack.
2) When you trip someone, they are prone. You can not trip someone who is already prone. Greater Trip does let you pull off one AoO when you trip, so having Combat Reflexes is good if you're a Monk that's going to flurry and trip multiple opponents.
3) If you trip first, then he is already prone. The AoO is against a prone opponent. That's the benefit of investing in those feats.
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On #1, the weapon focus feat & weapon enhancements only count for trip attacks if the weapon has the Trip ability. This is mentioned in the FAQ: Trip FAQ
Other Combat Maneuvers may not require having the related special ability to add these bonuses.
And, for the appropriate weapon, I believe that they stack because they are not the same kind of bonus, even though they both come from feats.
The +2 bonus from Improved Trip is actually untyped, so it will stack with any other bonus.
Note that the +2 untyped bonus from Greater Trip explicitly stacks with the +2 untyped bonus from Improved Trip, it says so in the feat description.
Also note that the +1 bonus from Weapon Focus is also untyped, and will therefore stack with other bonuses, as long as they are not also from Weapon Focus, and the weapon has the Trip special ability.
Whip: BAB, Str, Imp Trip, Grtr Trip, Wpn Fcs, Wpn Enh, Weapon Training
Longsword: BAB, Str, Imp Trip, Grtr Trip
Second Question, with the Second trip Feat (at lvl 6) can you use an AoO to attack the guy you just triped?
Yes, that's the biggest advantage to Greater Trip. You trip him, and he provokes. You (and anyone who threatens him) may make an attack of opportunity.
What if you used an AoO to trip him (and have Combat Expertise) do you get to do 2 AoO (one for trip and one for damage).
If you haven't tripped him yet, and he provokes (Say, for casting a spell, or moving out of a threatened square) then you may use your attack of opportunity to trip him. If you succeed, he provokes again.
If he's provoking by standing up from prone, then you cannot use the AoO to trip him, since he's still prone.
Dose the AoO of him going prone use his Prone AC or normal AC? (Prone is -4AC vs Melee)
An attack of opportunity is resolved before the action that caused it, so if you Greater Trip someone, you make your attack of opportunity -before- he's prone, so normal AC. If he provokes by standing back up, that AoO will be vs prone AC.