Let me try to help:
Weapon and Armor proficiency: Shinobi are proficient with all simple weapons, plus the kama, katana, kusarigama, nunchaku, sai, shortbow, short sword, shuriken, siangham, and wakizashi. They are proficient with light armor but not with shields.
Poison Use (Ex): At 1st level, a shinobi is trained in the use of poison and cannot accidentally poison herself when applying poison to a weapon.
This ability replaces track.
Ki Pool (Su): At 2nd level, a shinobi gains a pool of ki points, supernatural energy she can use to accomplish amazing feats. The number of points in the ninja’s ki pool is equal to 1/2 her shinobi level + her Intelligence modifier. As long as she has at least 1 point in her ki pool, she treats any Acrobatics skill check made to jump as if she had a running start. At 10th level, she also reduces the DC of Acrobatics skill checks made to jump by 1/2 (although she still cannot move farther than her speed allows).
By spending 1 point from her ki pool, a shinobi can increase her speed by 20 feet for 1 round. In addition, a shinobi can spend 1 point from her ki pool to give herself a +4 insight bonus on Stealth checks for 1 round. Each of these powers is activated as a swift action.
The ki pool is replenished each morning after 8 hours of rest or meditation; these hours do not need to be consecutive. If the shinobi possesses levels in another class that grants points to a ki pool, shinobi levels stack with the levels of that class to determine the total number of ki points in the combined pool, but only one ability score modifier is added to the total. The choice of which score to use is made when the second class ability is gained, and once made, the choice is set. The shinobi can now use ki points from this pool to power the abilities of every class she possesses that grants a ki pool.
This ability replaces the Slayer Talent gained at second level.
Slayer Talents: When a shinobi selects a slayer talent, she may choose any ninja trick whose effects are tied to her ki pool in addition to those she can normally choose.
This alters the slayer talent class feature.
Poison Immunity (Ex): At 11th level the shinobi becomes immune to all poisons.
This ability replaces the swift tracker class feature
Abundant Step (Su): At 13th level or higher, a shinobi can slip magically between spaces, as if using the spell dimension door. Using this ability is a move action that consumes 2 points from her ki pool. Her caster level for this effect is equal to her shinobi level. She cannot take other creatures with her when she uses this ability. Starting at 17th level this ability consumes only one point of ki. At 19th level the shinobi can spend 3 extra ki points to use this ability as a swift action or 2 extra ki points to take other creatures with her as normal per the dimension door spell.
This replaces slayer's advance, quarry and improved quarry.
If the intent is to completely subsume the ninja you can add these new Slayer Talents:
Swift Stike (Su): Prerequisite: Ki Pool. By spending 1 point from her Ki Pool the slayer can make an extra attack at her highest BAB as part of a full attack.
Ninja Steps (Ex): Prerequisite: Level 6. The slayer gains the No Trace and Light Steps abilities, using her slayer levels as her effective ninja level.
VM Mercenario, I was going to suggest something quite similar. I think taking away a couple Slayer Talents (or in this case adding optional slayer talents to gain functionality) is the best way to make Ki Pool balanced.