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Our DM is using the Hero Points optional rule where I can spend one point to make an additional attack.
My Ninja can spend one from his Ki Pool to make an additional attack.
At level one I took the Two Weapon Fighting feat.
Can I combine all three sources to make four attacks at level one? How many would be at -2 given that both weapons are Wakisashi?

The official hero points optional rule does not actually have an option for an extra attack—instead, a hero point may be expended for an entire extra standard action, which is quite a lot better. You can use that standard action for an attack, but you could also use it for other things.

The ki pool feature allows a ninja to expend a ki point for 1 extra attack at their highest BAB during a full-attack. There is no penalty associated with this.

The two-weapon fighting combat option allows you to make one extra attack with an “offhand” weapon, in exchange for a penalty on all attack rolls during that full-attack. The size of the penalty depends on whether or not the offhand weapon is light (the wakizashi is) and whether or not you have the Two-Weapon Fighting feat (you do). In this case, the penalty is −2.

And, of course, you start with a single attack by default.

That means you can make a full-attack, expending a ki point and using two-weapon fighting, to attack three times, all at −2. Two of those attacks must be with separate weapons; the third can be a second attack with either of them (or an attack with a third weapon if you really wanted to like kick or use armor spikes or something like that). After those attacks are finished, you can spend a hero point to get another standard action: you can use that to attack. Since it’s not part of the full-attack where you used two-weapon fighting, it does not take the −2 penalty, and is just made at your ordinary attack bonus.