This guide will be really lengthy and going over each mission individually, so if there is specific spots or missions you would like to jump to, press Ctrl+F and type in the name of a mission.

Delivery Service

Stand behind the wagon and let the enemies beat on it until the wagon is destroyed

The Missing Tamasaburo

Do this mission before Shop Assistant to get the Kunai skill plate earlier Use Choji to speed up any encounters you might run into on the way to Honeydew Mountain and use his Human Boulder to break the rock blocking the plant. Use a mix of projectiles and specials (Clones and Power Strike) to speed up the fight against Choji on the way back to the leaf village, as it's slightly stronger than using mainly normal combos. Pick up as much virtue as you can so you have a bit extra for more pieces for skill plate.

Shop Assistant

Switch Skill Plate to Kunai and buy Health Up (S), Tai-Attk +1 and +2, Stamina Up (S and M), and Defense +1 and +2. Put all the pieces in to boost stats before starting forced encounter.
Go through forced encounter, then farm for 7 more encounters to finish mission, since you need 8 fights to clear it. Use X+Square in midair then press Triangle after sliding on the ground to speed through encounters.

Fragile - Do Not Break

Same as Delivery Service, stand behind the wagon and let enemies destroy it as quickly as possible

Sensei for a day

Lure Konahamaru towards the Kunoichi and let him get beat up by them until he dies to fail the mission quickly.

Kakashi Training side mission

Naruto + Shikamaru vs Sasuke + Choji - Switch to Shikamaru and lock on to Sasuke to throw Kunai traps at him. Rinse and repeat for Choji as well until he dies, and refill stamina when necessary. Naruto + Choji vs Sasuke + Shikamaru - Switch to Choji and lock onto Shikamaru first and use Human Boulder on him until he dies. Rinse and repeat for Sasuke. If you send either of them airborne with the human boulder and have enough room to do it in a circle, hold up right or up left while locked on to keep them in a loop till stamina runs out.

Bad Publicity

Same as Shop Assistant, take the first forced encounter and then farm for 7 more so you have 8 when you finish. You should get the Leaf Skill Plate from clearing this mission and will be using this throughout the rest of the run. Use extra money from Shop Assistant + encounters from other missions and use it to buy Extra Clone A and B, Tai Attack +3 and Defense +3.

Hokage Dolls + Leaf Skill Plate Menuing

Use virtue to buy Tai Attack +4, Defense +4, Naruto U Barrage, and Air Dash. Fill in the Leaf Skill Plate and you should have enough space to where a Large piece and a small piece fit after filling it all in. When you get to Outskirts, switch to Kakashi when the big hoard of large enemies comes in, step back to get them closer and line them up to all get hit by Lightning Blade to quickly maul through them.

Prisoner Escort 1

Same as Delivery Service

Costal Disturbances

Safe Strat- After defeating all the enemies, keep your distance from Sasuke during the fight so you don't run into most of his combos and spam Naruto Uzumaki Barrage by holding R1 long enough for your clone gauge to be maxed out. Refill stamina with items when necessary to continue loop until Sasuke dies. Risky Strat-Position yourself behind Sasuke and use Naruto Uzumaki Barrage, use slide kicks to add to your combo after he falls to the floor to get extra stamina orbs off of drain effect, then quickly dash behind Sasuke and charge up clones while he recovers to set up another barrage. Repeat until Sasuke dies.

Gambler's Fallacy

Before heading out to the town to talk to the gambler, take Sasuke with you in your party. When you get to Monkeytail Mountain after fighting an encounter with the monkeys and triggering another one, switch to Sasuke and use Chidori on the monkey leader to quickly take him out. If he doesn't die, use clones and barrage to finish off the rest of his health before he disappears.

Sasuke Pursuit
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The Genjutsu Solution for Hakuten Inari should be ↑→→↑↑, but if you ever get confused, look at the shadows beside each of the gates. One of them should be facing towards the left while the others are on the right.
Keep your distance when Kabuto throws out his kunais as they deal major damage, and throw out barrages when possible. Run into his Underground Reflecting Fist Jutsu to speed up the fight if needed and catch him before he tries to heal.

Punishment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Same as Delivery Service

Sasuke's Challenge
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Use extra money from Gambler's Fallacy to buy Health up M and Empty Chip 1 from the store. Fill in the rest of the skill plate for a 50%+ Tai-Attack bonus before going into the fight. The fight should work the same as the one in Costal Disturbances, just rinse and repeat and keep your distance especially if you get the curse mark fight.

National Treasure
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Same as Delivery Service

Oil Fielder
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Same as Delivery Service

Prisoner Escort 2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Same as Delivery Service

Trouble in the sand
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Lock onto most of the enemies in forced encounters with Shikamaru and use Trap Kunais to quickly finish them off. Rinse and repeat till you get to the top of the tower and do the same for Gaara, though it can be kind of tricky since you have to bait out an attack or put him in midair/tumble to remove his sand armor. If you run out of items, try to get behind him and use remaining stamina for barrages or clones.

Hinata's Mission

When you return back to the town after getting the honeydew plant, keep your distance so you don't get hit as much and spam barrages on the giant ogre-like ninja to finish him off.

The Stuntman

Use Barrages and Neji's Rotation when forced to fight enemies, when you get to the fight with 2 praying mantises, stick to mainly using Rotation, as charging in with a barrage usually results in taking a big hit.

Prisoner Escort 3

Same as Delivery Service

Closed for Business

Take Choji with you before heading towards Blue Dragon Cave, when you have to make your way back out, there should be a path completely blocked by iron stones if you just head straight all the way through. Use Choji's Human Boulder to break them and quickly make your way to the cart section.
For the cart section, you want all the switches to be either all left or all right to make it to the end. If you have any trouble hitting them, using a standing triangle attack should help.

Mass Disappearances 

For the Gaara fight, you can usually have him bait out a sand clone and he'll drop his armor so you can hit him. Rotation deals more damage, but has a tendency to get blocked sometimes, so you'll want to be a little close to him with naruto and use barrages. For the Kabuto fight, you can run up to him with Neji and spam rotation. Do your next one right before he finishes getting up to put him into a loop until he dies.

Final Battle

Use any virtue you have left to boost your stamina and health to make it easier to survive incase you run into lengthy encounters on the way. When you get to the Kabuto + ogre-ninja fight, switch to Kakashi and use him and Naruto to take out the keystones. When all the keystones are gone, use Kakashi's lightning blade to quickly maul through both of them. For the fight with Orochimaru, switch to kakashi and use 1000 years of death to put yourself instantly behind him. Keep doing this every time right before he finishes getting up to put him in a loop until he dies, and the run is finished.