On the d20SRD, next to the "pick up an item," there is a FAQ linked that covers this. You can pick something up within your reach (which seems to qualify in this case) and it provokes an AoO. Notice that reaching into a threatened square doesn't provoke, just reaching while someone threatens you. So you don't have to be in their square, just be able to reach into it.
For purposes of evading the AoO, that's a different story. There's no way RAW ("Improved Pickup!") but it is certainly reasonable to allow an Acrobatics "move through opponent's square" check to do so. Of course you could always bull rush or otherwise move the opponent so they don't threaten you and then pick it up, or mage hand it, or a variety of other options - allowing innovation here is fine (attack it to move it, Sleight of Hand, etc.). Just make sure that enemies can also disarm and snarf the PCs' weapons as easily as they can...
Let's do a bit of set-up:
Charging
Charging is a special full-round action that allows you to move up to twice your speed and attack during the action. Charging, however, carries tight restrictions on how you can move...
Full-Round Action
A full-round action requires an entire round to complete. Thus, it can't be coupled with a standard or a move action...
Overrun
As a standard action, taken during your move or as part of a charge, you can attempt to overrun your target, moving through its square...
All emphasis mine. Links point to the d20PFSRD
So Overrun may be used it only 2 scenarios:
1. A creature is moving (as per the Move Action), and wishes to pass through another creature's square.
2. A creature wishes to Charge (move double it's Speed in a straight line) and to continue it's charging movement beyond it's target's occupied square.
Steps in the Overrun Process
Scenario (1)
1. A creature (A) takes a Move Action, but it's movement is blocked by another (B) that *does not grant A passage* through it's occupied square. (If granted passage, there is no point in using Overrun.)
2. A declares use of the Overrun combat maneuver, using up their Standard Action for that turn. A rolls a combat maneuver check against B's Combat Maneuver Defence (CMD).
On a successful roll:
3a. A may move through B's square unimpeded. If A is within range of another creature after their move they may not attack it as they have already used their Standard Action.
On a successful roll, 5 or more higher than the B's CMD:
3b. A may move through B's square and B is knocked prone, granting attacks of opportunity to nearby creatures. A may use their attack of opportunity to attack B, using their AoO for that round.[1]
On a failed roll:
3c. A's movement is halted in the previous square in their movement, adjacent to B. They may take any remaining actions (Swift or Free), and their turn ends. They may not attack B, as they have already used their Standard Action attempting to Overrun.
Scenario (2)
1. A declares B the target of a Charge (which is a Full-round action), but wishes to end their movement in a square beyond that occupied by B.
2. As per the specific rules of Overrun, A may use this maneuver as part of a Charge even though Overrun is usually a Standard Action, so A declares use of the Overrun combat maneuver in order to charge through B's occupied square.
On a successful roll:
3a. A may charge through B's square unimpeded. A continues to move in a straight line up to the maximum granted by the Charge. B was declared the target of the Charge, so no further attacks may be made by A against any other creature.
On a successful roll, 5 or more higher than the B's CMD:
3b. A may charge through B's square and B is knocked prone, granting attacks of opportunity to nearby creatures. A may use their attack of opportunity to attack B, using their AoO for that round.[1] A continues to move in a straight line up to the maximum granted by the Charge.
On a failed roll:
3c. A's movement is halted in the previous square in their movement, adjacent to B. They may not take any remaining actions (except Free Actions) because their Full-round Action has failed, and their turn ends.
Bonus Scenario!
A wishes to declare a Charge against creature B, but another creature (C) occupies a square between A and B.
A cannot declare a Charge against B, because of this specific rule from Charging:
You must have a clear path toward the opponent... If any line from your starting space to the ending space passes through a square that blocks movement, slows movement, or contains a creature (even an ally), you can't charge.
- Instead, A decides to declare a charge against C and attempts to Overrun. A's Combat Maneuver Check is successful, so A continues to charge up to their max movement (as granted by the Charge; movement must remain in a straight line). If A ends in a square adjacent to B, A may not attack B as they have used up their actions for this turn; they must wait until the next round and their next turn..
In Sum, to answer your direct questions
1. Yes and No. You don't take a Standard Action to enter their square. There are also two (slightly) different uses of the maneuver, as I've outlined. If charging, the target of the Overrun is also the target of the Charge. Overrun does provoke an AoO unless you have the feat. The other various minor details were also correct. As a side note, I found it odd to describe Overrun's use from the perspective of the target, and have outlined my answer slightly differently.
2. Yes, as per the rule of specificity. It's worth noting that while Overrun does allow you to break your move with a Standard Action, this does mean it uses up your Standard Action and you can't take another until your next turn. (So no attacks after your movement has ended.)
3. No. You don't/can't overrun a creature in order to charge another. The target of the charge is also the target of the overrun. Overrun just allows you to pass through their square; you essentially trade an attack against the creature for mobility on the battlefield. It's also No if moving, as you only have one Standard so you cannot attack after the overrun attempt is made, regardless of success or failure.
4. No. For the same reason as (3), and also for the fact that you cannot target more than one creature with a Charge.
[1]: An attack of opportunity "interrupts" the normal flow of actions in the round. If an attack of opportunity is provoked, immediately resolve the attack of opportunity, then continue with the next character's turn (or complete the current turn, if the attack of opportunity was provoked in the midst of a character's turn). (d20PFSRD)
Best Answer
Picking up an item is neither faster nor easier because a creature's prone
A prone creature doesn't pick up an item in less time than a standing creature, and a prone creature still provokes an attack of opportunity from each foe that threatens the creature when it attempts to pick up an item.
Despite the weapon being right there on the ground and in the prone creature's space, if the creature has been the victim of the combat maneuver disarm, then the typical creature must take a move action that provokes attacks of opportunity to pick up the weapon. (Also see the Table: Actions in Combat and its short accompanying FAQ entry.)
Note: The fighter in question has picked here the right order in which to execute these maneuvers: If the fighter's trip combat maneuver succeeds and renders the foe prone, when the fighter makes the disarm attempt against the prone foe, Combat Modifiers has the foe suffer a −4 penalty to his Combat Maneuver Defense score as "[a]ny penalties to a creature's AC also apply to its CMD.")