Follow the usual route as always, i'll mark specific points where you can farm trust to a very high degree in parts of the story. Keep in mind that melee-destroying/grenading regular robot infantry can usually result in an increase in the trust levels, another good tactic is to decapitate security robots so that they too often decapitate their fellow brethren and usually get in close while shooting at eachother, making for the perfect opportunity to melee-kill both of them once they're close to eachother whenever they're in the process to sync-melee eachother as said melee double-kill can usually spring forth a trust increase (when it's done by you, not the two headless security robots, just to clarify), do either whenever possible as it can usually, not "always", result in an increase in trust levels, obvious when it happens for when teammates say specific dialogue such as: "That was SWEET! Whoa! Where did THAT come from?? Words fail to express your magnificence! Danny-boy! A freakin' Star, man!" and so forth. Destroying enemies with gunfire can do the trick as well, but is not as effective as the grenade/melee trick however, making it somewhat unreliable when you want to build up trust, it still happens from time to time though, just not as much as when you melee/grenade enemies of course, just something to keep in mind. ^^; Coupled with this is the fact that all teammates, excluding Shindo of course, must... MUST have their trust bars set at level four at maximum, you can usually tell if it's at level four if you see four bars on the left-most side of the screen, indicating how many bars worth of trust you have with your current teammates. Now I shall go into detail about certain parts in the story where you can farm a good amount of trust to build up those specific party members' trust gauges.

EDIT: I completely forgot about it, but there's someone in the underground mall (The area where you chill out for a while that has Yuki in it.) that sells you a Trust Enhancement nanomachine that doubles the amount of trust you get for those in your current squad. Buy it (It's not that expensive, just 500 credits.) and equip on Dan for good to have the following trust effects boosted.

EDIT2: Decided to add in the "Decapitation" method explained above as it's another useful way to farm trust most of the time.

Chapter 2-4: At the part where Yuki is unlocking the door you will face a set number of regular security robots that, at first glance, seems to respawn infinitely. This is not the case as they will eventually stop spawning, use their vast spawning numbers to increase Charlie and Rachael's trust gauges as much as possible (I use them here, for reasons i'll include in a later bit describing which teammates you should pick for when it asks you to choose your teammates to take with you) using the aforementioned tricks.

Chapter 2-4: Here you will face a carrier-type boss, meaning that it spawns an infinite amount of aerial robots in which to fight as well as an infinite amount of Whirlers that transport rocket ammunition so that you won't run short of Stinger missiles and need to resupply them from Whirlers carrying them. Use the infinite amount of aerial enemies to your advantage by using the Stinger to pre-lock on a foe excluding the boss' four main engines to keep up the infinite-spawning enemies to build up Charlie and Rachael's trust gauges as much as you can as this is one of the few parts in the story where enemies spawn infinitely, keep this up and you won't have to worry about Rachael and Charlie's trust gauges when you seperate from them later on. To get a good percentage of trust increase, wait until the aerial drones group together, then launch the pre-locked-on missile at a false target but close enough to a group of aerial drones so that it hits the group of bunched-up aerial drones instead of the far-away target to be more guaranteed to get more trust increases for both Charlie and Rachael.

Chapter 2-5: After you go back to save the other two teammates who got trapped in the sewers and go to the elevator an infinite amount of robot monkeys appear and it is at this point you can build up a vast amount of trust on the two opposite of Rachael and Charlie that you left in the sewers, use your rifle ammo carefully here as there are no Shop Terminals during the infinite spawning robot monkeys event here. There is, however, a Bosonic Energy recharging spot near the elevator exterior so use that when you're near/out of rifle ammo to even the odds against those pesky robot monkeys so you can continue building up Bo and Faye's trust gauges (again, explained later).

Chapter 3-2: At this part you have to hold your ground against several regular security robots plus an artillery robot known as a "Mobile Gun" (keep in mind that, like all artillery is, it cannot fire at close-range targets, something to keep in mind if you want to avoid its deadly rocket fire) and afterwards Bo tells you to go on without him after holding your own against the enemy, ignore him and stay since, like in Chapter 2-4 with Yuki unlocking the doors, there is a good amount of spawning security robots, but, like Chapter 2-4, they are not infinite like the robot monkeys and aerial drones were. Keep this in mind and you can exploit the Shop Terminal to keep buying Frag Grenades to spam-throw grenades at the enemy on the upper level of where they spawn near to get as much trust attained as you can for Cain and Bo, you'll know you've depleted them all once the metallic door closes.

Chapter 5-1: There are a number of security robots that spawn during the Medusa (Mecha-tentacle Chandelier hybrid) boss fight on the balcony level, as such you can feel free to utilize the above tactics to gain more trust-ups with the remaining team you are with.

The teammates I choose for when it asks you to choose what teammates you want to have with you are as follows:

Chapter 2-1<Charlie/Rachael> Chapter 2-2<same as Chapter 2-1> Chapter 2-4<same as Chapter 2-1> Chapter 3-2<Bo/Cain> Chapter 3-4<Cain> Chapter 4-1<Cain> Chapter 4-3<Cain> Chapter 5-2<Faye/Shindo>

With this setup and enough exploiting the aforementioned tricks towards building up the trust gauges to max you'll be able to get the Good/Best ending with little to no stress, hope this guide helped. :) Also, keep in mind that after some battles one of your teammates may either congratulate or berate you based on your performance in the battle, getting battles done well enough using grenades, getting decap headshot chains, mowing down foes quickly with gunfire and/or a good amount of finishing melees will usually have the former happen and also some choices might lower their trust gauge so choose the right choice when they congratulate you to raise their trust meter further.