What is this build for exactly?
Looks like its spec'd for PvP.
Just my guess.
Lol, its for fun? shooting for softcapped defense to all positions. Thats about it. This is coming from a SR scrapper point of view, btw. Never touched a stalker and have no clue what the point is. I figured lots of stealth and hit hard?
I figured this for a PvE build, and why not? My CoV beta character was a Ninjitsu Stalker and the recent buffs have made Stalkers a lot more playable.
You can manage capped melee defence if you slot your attacks with two full sets of Touch of Deaths and two full sets of Obliterations. That's an extra 18% defence to melee. It won't be cheap. 
Also drop Blinding Powder. It sounds good on paper but it's really disappointing in practise. You want capped positional while you work to buy those sets? It's right there in Kuji-in Retsu. It's Elude!
Also I don't know if you're committed to Mako, but if you take Soul Mastery instead you can get Shadow Meld at 44 which is a mini-Retsu that will also cap positional defense.
"He may be arrogant, but he happens to be correct" - Ellis
"The server is full of crazies" - New_Dark_Age
Rainbow Arcana / Diamond D: Legion of Freedom - Virtue
lof.guildportal.com
Blinding Powder confuses, sleeps, lowers -tohit. Yes, it's only mag 2. That's still fewer minions getting that chance (5% at soft cap) to hit you with defense debuffs and other effects. The confusion makes it an additional damage source. Plus it can even help the team's survivability--I know it certainly does when I get sidekicked up to my friend's Nin stalker to kill Rikti and stuff.
It's up to you though. I know I haven't gotten it yet--my Stalker's only 28. My friend seems to use it to good effect, but use your own judgment. Maybe try it out and form your personal opinion?
I love Blinding Powder.
It's fun to mess with a mob before ripping their kidney out. And as Alef said, it helps making you that much more unhittable. And you could always use it as a IO mule.
I would personally just get range and AoE IO bonuses first, relying on Parry to provide the melee defense. With it 3 slotted with defense IOs, you should be soft capped with just 1 application of it.
Then later if I wanted to drop Parry, then shoot for melee defense bonuses.
Parry is quite nice. Can really jack up your melee defense up to 71% at level 32 (I'm working on one myself).
Here is my first run BS/Nin build. I have no clue where the defense values actually are but I know they are close.
Villain Plan by Mids' Villain Designer 1.601
http://www.cohplanner.com/
Click this DataLink to open the build!
Level 50 Natural Stalker
Primary Power Set: Broad Sword
Secondary Power Set: Ninjitsu
Power Pool: Fitness
Power Pool: Leaping
Power Pool: Concealment
Ancillary Pool: Leviathan Mastery
Villain Profile:
Level 1: Hack -- C'ngImp-Acc/Dmg(A), C'ngImp-Dmg/EndRdx(3), C'ngImp-Dmg/Rchg(5), C'ngImp-Acc/Dmg/Rchg(9), C'ngImp-Dmg/EndRdx/Rchg(15), Mako-Acc/EndRdx/Rchg(34)
Level 1: Hide -- LkGmblr-Def(A), S'dpty-Def(31), LkGmblr-Rchg+(36), S'dpty-Def/EndRdx(45)
Level 2: Ninja Reflexes -- S'dpty-Def(A), S'dpty-Def/EndRdx(3), GftotA-Def/EndRdx(9), GftotA-Def(37)
Level 4: Danger Sense -- S'dpty-Def/EndRdx(A), S'dpty-Def(5), GftotA-Def/EndRdx(11), GftotA-Def(36)
Level 6: Assassin's Slash -- C'ngImp-Acc/Dmg(A), C'ngImp-Dmg/EndRdx(7), C'ngImp-Dmg/Rchg(7), C'ngImp-Acc/Dmg/Rchg(15), C'ngImp-Acc/Dmg/EndRdx(17), Dmg-I(25)
Level 8: Build Up -- AdjTgt-ToHit(A), AdjTgt-ToHit/Rchg(11), AdjTgt-EndRdx/Rchg(13), AdjTgt-Rchg(42), AdjTgt-ToHit/EndRdx/Rchg(42)
Level 10: Swift -- Run-I(A)
Level 12: Placate -- RechRdx-I(A), RechRdx-I(13), RechRdx-I(25)
Level 14: Health -- Numna-Heal(A), Numna-Regen/Rcvry+(46), Mrcl-Heal(46), Mrcl-Rcvry+(48)
Level 16: Kuji-In Rin -- RechRdx-I(A), RechRdx-I(17)
Level 18: Parry -- C'ngImp-Acc/Dmg(A), C'ngImp-Dmg/EndRdx(19), C'ngImp-Dmg/Rchg(19), C'ngImp-Acc/Dmg/Rchg(31), C'ngImp-Acc/Dmg/EndRdx(31)
Level 20: Kuji-In Sha -- S'fstPrt-ResDam/Def+(A), ImpArm-ResDam/EndRdx/Rchg(21), ImpArm-ResDam/Rchg(21), Numna-Heal(40), Numna-Heal/Rchg(40), Numna-Heal/EndRdx/Rchg(40)
Level 22: Stamina -- P'Shift-End%(A), P'Shift-EndMod(23), EndMod-I(23), EndMod-I(39)
Level 24: Combat Jumping -- Zephyr-Travel(A), Zephyr-Travel/EndRdx(39), Zephyr-ResKB(45)
Level 26: Disembowel -- Mako-Acc/Dmg(A), Mako-Dmg/EndRdx(27), Mako-Dmg/Rchg(27), Mako-Acc/EndRdx/Rchg(29), Mako-Dam%(29), Mako-Acc/Dmg/EndRdx/Rchg(36)
Level 28: Super Jump -- Zephyr-Travel(A), Zephyr-Travel/EndRdx(37), Zephyr-ResKB(37)
Level 30: Smoke Flash -- RechRdx-I(A), RechRdx-I(46)
Level 32: Head Splitter -- Mako-Acc/Dmg(A), Mako-Dmg/EndRdx(33), Mako-Dmg/Rchg(33), Mako-Acc/EndRdx/Rchg(33), Mako-Acc/Dmg/EndRdx/Rchg(34), Mako-Dam%(34)
Level 35: Blinding Powder -- Cloud-ToHitDeb(A), Cloud-%Dam(42), Cloud-Acc/Rchg(48), Cloud-ToHitDeb/EndRdx/Rchg(48), RechRdx-I(50)
Level 38: Slice -- Sciroc-Acc/Dmg(A), Sciroc-Dmg/EndRdx(39), Sciroc-Dmg/Rchg(43), Sciroc-Acc/Rchg(43), Sciroc-Acc/Dmg/EndRdx(43), DefDeb-I(45)
Level 41: Water Spout -- RechRdx-I(A)
Level 44: Hibernate -- RechRdx-I(A)
Level 47: Stealth -- LkGmblr-Def(A), LkGmblr-Def/EndRdx(50)
Level 49: Caltrops -- Posi-Dmg/Rchg(A), Posi-Dam%(50)
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Level 1: Brawl -- Empty(A)
Level 1: Sprint -- Empty(A)
Level 2: Rest -- Empty(A)
Level 1: Assassination