Learning the timing is up to you,Arsenal,but here's a list of option u can do w/ each character you mentioned (all can do RH, Uppercut, aa-Sweep, aaHP or s.HK but unless mentioned, it's either "meh" or not the best option):
Kabal - Spin, uppercut, RH (both have excellent properties), aa-Sweep, [aaHP, Spin, aaHP,HP, JK/AFB ] <----preferred, 49%
Stryker - Baton Throw (F,F+HK), [aaHP,HP, Riot Gun, Baton Throw(whiff), aaHP,HP, Riot Gun.....cont.], s.HK, aa-Sweep
Liu Kang - Uppercut, RH (best in game), s.HK, jump back AFB, [aaHP,HP, JK, AFB (Flying Kick on some)]....52%, i think.
Kano - [aaHP, JK, Air Throw], s.HK, aa-Sweep, (incredibly good), Upward Cannonball, [aaHP, Grab n' Choke], "instant" Air throw, [aaHP,HP, Blade Swipe]
Scorpion - [aaRH, Teleport, (aaLP/HP) Spear, HP,HP,HK,B+HK], <--aaLP/HP won't connect on everyone, [aaHP,HP, JK, Teleport, SPear, HP,HP,HK,B+HK] (both are a little over 50%). RH always is great for ninjas but try to combo from it for better%
Ermac - [aaRH, Teleport, (aaLP/HP), TKS, aaRH, Teleport, aaLP/HP, Fireball/JK/HK ], .... [aaHP,HP, JK, Teleport, TKS, aaHP,HP.....aaHP, JK (or Fireball)]......aaHP, TKS, aaHP,HP, JK, TKS, aaHP,HP, ....aaHP, JK (or Fireball)] <--most damaging
Human SMoke: fuck writting all this again lol, just read the link:
http://blackdragonmk.proboards.com/index.cgi?board=umk3&action=display&thread=401&page=1
C. Sub - aaHP, Ground Freeze, SUJK, HP,HP,D+LP,D+HP...runburst, aaHP,HP, JK/s.HK
Reptile - (aaHP,HP),Forceball, aaHP,HP, Forceball, into infinite (or finisher of choice)
That's all I can think of atm, idk if u include Unmasked Sub as a male ninja but I don't cuz he's very different in properties, but I can go over him too if u need it.