Please help the community by disproving any information in the following guide by commenting with visual proof if possible. We are still looking to fill out the complete Ninja weapon mod slot pool, with specifics needed for the Arrow and Riser mod slots unique to the Yumi.

When you craft mods for weapons, every mod will come with a Bonus Ability that will be enabled once that mod is upgraded to Level 3. The chance to roll a particular ability is unknown, and seemingly completely random. It is also unclear if certain mods on certain weapons have restrictions on which abilties can potentially roll. (Edit 7/25: Based on my limited testing, I am now relatively confident that certain abilties can only be rolled on certain mod slots, but there is some crossover where the same abilties can roll on multiple slots. I will be exploring this in a section below.)

As far as we are currently aware, mod bonus abilities are:
1. Only active on the weapon equipped with said mods. (Tested on 7/26; had pistol with Deadly Resupply, primary would not regen ammo)
2. Stack with each other, up to three copies (confirmed by TW Molly https://psteamcommunity.yuanyoumao.com/app/1430190/discussions/0/594029415763279235/)

General Flat Damage Bonuses

Ammo Efficiency: Increase damage by 7 when magazine is at or below 1/4 capacity
Critical Exposure: Next round deals 10 additional damage after destroying an enemy's limb or armor
First Strike: Increases damage by 35 from first shot with a fully loaded magazine
Surrounded Strike: Bonus 5 damage when within 10m of 3 or more enemies

General %-Damage Bonuses

Combat Coordination: Deal 3% bonus damage when within 10m of at least 1 teammate
Coordinated Carnage: Teamates within 10m gain 3% Damage buff for 3 seconds after killing an enemy
Critical Strikes: Each shot has 1.5% chance to deal 150% damage
Last Stand: Deal 4% additional damage when at or below 20% HP
Long Distance Operator: Deal 2% bonus damage when no enemies within 10m
Squad Strength: Gain 1% bonus damage for each teammate within 10m

Melee Bonuses

Melee Master: Deal 2.5% more Melee Damage and 20% more bash damage
Zed Time Rampage: Increases Melee and Bash damage by 20% during Zed Time

Boss Related Bonuses

Boss Basher: Deal 5% more damage to bosses
Boss Bash Team-up: Teammates within 10m deal 5% bonus damage against bosses
Boss Buffer: Damage from bosses reduced by 5%

Status Effect Powers

Panic Attack: +10 Panic Power
Stumblesome: +20 Stumble Power
Toxicity: +15 Toxic Power

Healing/Survival Bonuses

Armor Repair: 3% chance to refill armor to 20% after destroying enemy's limb or armor
Armored Allies: Teammates within 10m have a 5% chance to gain 5 armor after killing an enemy
Blood Transfusion: Regen 1 HP/s while below 25% HP
Bounce Back: 4% chance to immediately restore 50% of damage received after each hit taken
Killshot Cure: Teammates with the lowest health within 10m gain 1 HP after killing an enemy

Personal On-Kill Effects

Combat Cure: 3% chance to heal 5% HP on a killshot
Deadly Resupply: 33% chance to return 1 round to the magazine on a killshot
Kill Shield: Reduce incoming damage by 5% for 5s on a killshot

Zed Time Bonuses

Allied Zed Time: Zed time gain multiplier is increased by 15% if at least 1 teammate is within 10m
Deadlier Zed Time: Teammates within 10m deal 2.5% bonus weapon damage during Zed Time
Zed Time Reload: 20% chance to fully refill magazine from reserves after Zed Time triggers

Miscellaneous

Agile Aiming: Reduce spread while moving by 10%

This lists all the above Bonus Abilities by the slots they can be potentially crafted in. Bolded abilities are what I personally believe are high priority ones to craft and prioritize on slots. Some of these will conflict, and it will be up to you to decide which ability deserves the slot. Some are more important for pre-boss waves, and some are more important for dedicated boss builds. Your priorities will also be different if you are using a DPS class versus a support Medic.

Special thanks to u/Nisae32 and Kenndrik

Ammo Efficiency, Armor Repair, Armored Allies, Combat Cure, Critical Exposure, Critical Strikes, Deadlier Zed Time, Deadly Resupply, First Strike, Panic Attack, Squad Strength, Stumblesome, Surrounded Strike, Toxicity, Zed Time Reload

Agile Aiming, Allied Zed Time, Armor Repair, Blood Transfusion, Boss Buffer, Combat Coordination, Coordinated Carnage, Deadlier Zed Time, Deadly Resupply, Kill Shield, Last Stand, Long Distance Operator, Melee Master, Stumblesome, Zed Time Rampage

Agile Aiming, Allied Zed Time, Ammo Efficiency, Armor Repair, Armored Allies, Blood Transfusion, Boss Bash Team-Up, Boss Basher, Bounce Back, Coordinated Carnage, First Strike, Kill Shield, Killshot Cure, Last Stand, Melee Master, Zed Time Rampage

Armored Allies, Boss Bash Team-Up, Boss Basher, Boss Buffer, Combat Coordination, Critical Exposure, Critical Strikes, Deadlier Zed Time, Kill Shield, Killshot Cure, Last Stand, Long Distance Operator, Panic Attack, Squad Strength, Surrounded Strike

Allied Zed Time, Ammo Efficiency, Blood Transfusion, Boss Basher, Boss Buffer, Bounce Back, Combat Cure, Critical Exposure, Deadly Resupply, First Strike, Long Distance Operator, Squad Strength, Surrounded Strike, Toxicity, Zed Time Reload

Agile Aiming, Armored Allies, Boss Bash Team-Up, Bounce Back, Combat Coordination, Combat Cure, Coordinated Carnage, Critical Strikes, Killshot Cure, Melee Master, Panic Attack, Stumblesome, Toxicity, Zed Time Rampage, Zed Time Reload

Armor Repair, Boss Basher, Combat Coordination, Coordinated Carnage, Killshot Cure, Long Distance Operator, Melee Master, Squad Strength

Blood Transfusion, Boss Buffer, Bounce Back, Kill Shield, Last Stand, Melee Master, Panic Attack, Surrounded Strike,

Boss Basher, Boss Buffer, Bounce Back, Combat Coordination, Combat Cure, Panic Attack, Toxicity, Zed Time Rampage

Blood Transfusion, Boss Buffer, Combat Cure, Kill Shield, Last Stand, Panic Attack, Surrounded Strike, Zed Time Rampage

Bounce Back, Combat Coordination, Kill Shield, Last Stand, Melee Master, Surrounded Strike, Toxicity, Zed Time Rampage

Allied Zed Time, Armored Allies, Boss Team Bash-Up, Critical Exposure, Critical Strikes, Deadlier Zed Time, Long Distance Operator, Stumblesome

Allied Zed Time, Armor Repair, Boss Basher, Combat Cure, Critical Exposure, Deadlier Zed Time, Killshot Cure, Stumblesome

Armor Repair, Armored Allies, Boss Bash Team-Up, Coordinated Carnage, Critical Strikes, Killshot Cure, Long Distance Operator, Squad Strength

My personal opinion is that bonuses like Boss Bash Team-Up (best bonus currently in game IMO), Boss Basher, Boss Buffer, Squad Strength, Combat Coordination, Deadly Resupply (pre-boss wave) are the best-in-slot bonuses currently available. Thus, we need to find out how many potential slots these preferred bonuses can roll on. Below is a list of confirmed bonuses rolled on specific slots on specific weapons.

• Current trends indicate that ability "buckets" (wherein a certain number of abilties can roll on a specific mod slot) exist across weapons. For example, Ammo or Barrel mods roll with the same potential Bonus Abilties regardless of which weapon you craft for.
  
• It seems that 15 bonuses, or half the entire pool of 30, can roll on the Ammo slot. This may be the maximum of all slots, and would make logical sense, but still unconfirmed as of 7/28.
  
• Boss Bash TeamUp found on three guaranteed slots currently, Underbarrel, Sight and Internal. Getting three of these mods on any weapon you are fighting with during the boss wave should be priority #1.

Medic KH-380 Sidearm testing:
Ammo can roll: Deadly Resupply, Squad Strength, Deadlier Zed Time, Zed Time Reload, Panic Attack, Armored Allies, First Strike, Toxicity, Ammo Efficiency, Surrounded Strike, Critical Exposure, Squad Strength, Armor Repair, Critical Strikes,
Internal can roll: Killshot Cure, Bounce Back, Boss Bash TeamUp

LF-85 testing:
Ammo can roll: Squad Strength, Zed Time Reload, Critical Exposure, Deadly Resupply, Critical Strikes, Deadlier Zed Time, Armored Allies, First Strike, Panic Attack, Surrounded Strike, Toxicity, Armor Repair, Ammo Efficiency, Combat Cure, Stumblesome
Barrel: Coordinated Carnage, Boss Buffer, Stumblesome, Ammo Efficiency
Underbarrel: Melee Master, Ammo Efficiency, Kill Shield, Coordinated Carnage, Agile Aiming, Armor Repair, Blood Transfusion, First Strike, Boss Basher, Allied Zed Time, Zed Time Rampage, Bosh Bash TeamUp
Sight: Long Distance Op, Kill Shield, Killshot Cure, Critical Strikes, Panic Attack, Last Stand, Armored Allies, Deadlier Zed Time, Boss Bash Team-Up
Magazine: Boss Basher, Critical Exposure, Surrounded Strike, Ammo Efficiency, Deadly Resupply, Squad Strength, Toxicity, Long-Distance Operator
Internal: Armored Allies, Melee Master, Agile Aiming, Coordinated Carnage, Stumblesome, Toxicity, Killshot Cure, Critical Strikes, Zed Time Rampage, Panic Attack, Team Boss BashUp

MP6 Testing:
Underbarrel can roll: Boss Bash TeamUp (!!), Killshot Cure, Allied Zed Time

Kunai testing:
Coating can roll: Boss Basher, Long-Distance Operator, Killshot Cure, Combat Coordination, Melee Master, Armor Repair,
Grip: Melee Master, Blood Transfusion, Panic Attack, Boss Buffer, Surrounded Strike, Panic Attack, Last Stand,
Blade: Bounce Back, Toxicity, Boss Basher
Quiver: Long-Distance Operator, Boss Bash Team-Up

Vulcan TA testing, courtesy of Videl:
Ammo can roll: Armor Repair, Critical Strikes, Toxicity, Panic Attack, Stumblesome, Zed Time Reload, Squad Strength, First Strike, Deadly Resupply, Surrounded Strike, Deadlier Zed Time, Combat Cure
Barrel: Long Distance Operator, Boss Buffer, Stumblesome, Deadlier Zed Time, Last Stand, Blood Transfusion, Melee Master, Allied Zed Time, Coordinated Carnage, Agile Aiming, Combat Coordination
Magazine: Critical Exposure, Surrounded Strike, Ammo Efficiency, Boss Basher, Combat Cure, Deadly Resupply, Squad Strength, Blood Transfusion, Toxicity, Long Distance Operator, First Strike, Bounce Back, Boss Buffer
Internal: Toxicity, Armored Allies, Panic Attack, Melee Master, Combat Cure, Boss Bash Team-up, Agile aiming, Killshot Cure, Zed Time Rampage, Critical Strikes

IR-50 Brimstone testing, courtesy of Videl:
Ammo can roll: Armored Allies, First Strike, Deadly Resupply, Critical Strikes, Panic Attack, Deadlier Zed Time, Squad Strength, Toxicity, Zed Time Reload, Combat Cure, Surrounded Strike, Ammo Efficiency, Stumblesome.
Barrel: Killshield, Armor Repair, Last Stand, Coordinated Carnage, Allied Zed Time, Blood Transfusion, Agile Aiming, Long Distance Operator, Combat Coordination, Boss Buffer