Although it'd be easier to just write a fanfic retaining almost nothing from the original version of the story, I'll try to keep the main players' designs and origins the same or almost the same while fixing the major problems:
Firstly, I'd start off the Trunks flashback almost the same as the original, but with Trunks training using Bulma's gravity chamber to explain his greater GAINZ while using the Z-Sword. I'd also add a panel where Kaioshin whispers to Kibito if it's a good idea to not let Trunks know about the healing powers that come with becoming a Kaioshin's disciple, where Kibito assures him that learning to harness that power would only interrupt his training to increase his power, and that since Kibito himself can heal them, it's better to not distract him. There, plot hole in regards to Trunks not knowing he can heal people plugged. I'd also add that Dabura has been training for the decade+ that they spent in space to ensure this plan can succeed, so that Dabura keeping up with and even outperforming this stronger version of Trunks makes sense.
Zamasu's origin story is one where I'd make the most drastic change. Instead of him going evil from just seeing barbarians kill each other, I'd instead have it so that Zamasu was a Kaio who had nothing but benevolent intentions at first, and when he saw mortals genuinely yearning to prosper and grow through sending satellites to outer space to overcome their home planet's harsh weather conditions, he tried to help them achieve this cause by offering god-given wisdom in building advanced spaceships. He had hoped that this would help other civilizations then learn from their positive attitude, yet when offered this pinnacle of technology, the civilization instead enslaved a powerful Barbarian warrior race and mass-produced spaceships to spread nothing but bloodshed and chaos onto planets all over Zamasu's galaxy, before then putting their entire universe into disarray. Not knowing what to do, Zamasu enlisted Gowasu's help and was promoted to being his disciple so that he could help the righteous among these mortals heal from their wounds and put a stop to this meaningless bloodshed, yet the Barbarians then took this opportunity to break the advanced civilization's mind control and stole their technology, and then allied themselves with another warfaring, naturally powerful race and went on to enslave the entirety of Universe 9 before going on to kill people of other races simply to satisfy their thirst for slaughter.
Fortunately, a select few among the Barbarians saw that this wasn't right and earned Zamasu's trust, and for their courage Gowasu awarded them his two Potara earrings so they could merge and finally put a stop to this madness - however, this effort was all for naught because it turned out that a rival clan of these warriors had rebuilt the brainwashing technology that was formerly used to enslave the Barbarians themselves, and forced the two most powerful warriors to kill their own families before turning on Gowasu and Zamasu and nearly killing them. Zamasu is able to utilize a clever use of Gowasu's Time Rings to travel just one second into the future and sneak up on the two warriors and break the mind controlling technology, yet when the trauma of their memory of killing their own families was restored, the two went on to slaughter their own kinsmen in rage before then beating on each other. Zamasu at this point has resolved to destroy the planet and end these two once and for all, but Gowasu points out to the three of them upon paralyzing them with his Kaioshin power that the principle of the Kaioshin is that with the help of allies, one can become a force larger than oneself, and it is through goodwill and forgiveness that solidarity and unity can be born to restore peace - and that was the intent that the first of the Kaioshin had when crafting the symbol of the Kaioshin's authority - the fusion Potara earrings. However, in their thirst to cause more bloodshed to vent their anger the two Barbarians misuse this information to then merge with each other with the Potara, and then easily reduce Gowasu and Zamasu to half-dead, broken bodies before then announcing their intent to use the spaceships to bring the whole universe to their heel and kill, rape and plunder as they wish. Gowasu, in his last defiant breath, attempts to destroy their Potara to ensure that this madness will end in an hour, but they simply kill him.
Now consumed by a blind rage, Zamasu unlocks all his potential power as a Kaioshin and restores his own wounds before attacking the evil fusion, but merely ends up being tortured for the next hour and is told that he and Gowasu were the ones who created this monster, and they'll rue their mistake in Hell for the rest of eternity. With his last bit of strength Zamasu stabs the fusion in the neck and seemingly causes him to defuse (upon which he takes the Potara earrings as Gowasu's memento), yet when he lets down his guard upon doing so, the unfused halves reveal the wound was negated by the two defusing and then seemingly kill Zamasu before fleeing on a spaceship to continue their quest to quench their madness, hatred and thirst for bloodshed. Zamasu somehow survives even this and then realizes that everything he did to try and help humanity only reduced his universe to nothing but a land of madness - and so he begins to watch GodTube to seek out the strongest mortal body possible to exact his revenge - which happened to be the Super Saiyan Blue body of Goku's, as he saw in the U6-U7 tournament broadcast. Zamasu travels to Universe 6 and Universe 7 and then steals Goku's body, after which he kills all mortal life in Universe 9 by using his undying rage to become a Super Saiyan and travels to Future Trunks' future as Goku Black.
After this, he manages to brainwash his future self (who didn't encounter this massacre because Beerus happened to wake up later than in the BoG arc in this timeline and just erased the planets described above in Zamasu's backstory when hearing that
's universe was seeing unprecedented chaos) into joining his cause by implanting his memories into Future Zamasu. This experience and the ensuing grief unlocks Future Zamasu's latent potential as well, yet due to him seeing no need to steal a mortal's body due to not ultimately sharing the same experiences, he instead just seals Future Gowasu into the core of their Kaioshin-kai to prevent him from meddling. The two then begin the Zero Mortals Plan.
Most of the conflict can then go the same as they did in the Super manga, except that I would have the Black = Zamasu reveal not be made until they fight Black a second time like in the anime. And I would have Trunks not turn SSJ Ikari but use Taiyo-ken to escape the Zamasus when Black becomes Rose, with his usage of it being stated to be because he fell for the attack twice against Cell and therefore saw the need to learn it rather than him being so incompetent as to be done in by his own technique twice in the Cell arc.
And rather than the Mafuba failing because Goku forgot the seal, the jar in which Future Zamasu got sealed would instead be destroyed by a near-dead Black, who straight after Zamasu becoming free just puts his earring on his other ear to fuse as a last resort. I'd then have Merged Zamasu arrogantly allow the heroes to heal using his own power just to make their defeat that much more devastating (which explains how Goku can spam SSJB), and Vegetto would manage to erase all of Merged Zamasu using his Final Kamehameha, only for Zamasu to reveal that he can regenerate from the hands that Vegetto cut off and stab Vegetto's spine with a sneak attack - causing the fusion to dissolve rather than it dissolving in like 3 minutes from SSJB's strain.
After that, I'd have Vegeta instead of Goku become PSSJB, with him being only able to do it because Goku had the idea before him, yet lacked the necessary training to achieve it while Vegeta was able to thanks to his RoSaT training. He'd still get stomped by Zamasu, yet Goku and Trunks managing to combine their Taiyo-ken to completely immobilize Zamasu allows Vegeta to get him in a full nelson, allowing Goku to then seal Zamasu and Vegeta together by having
retrieve a copy of the amulet and bottle from Kami's Palace (the one he used on Majunior in the 23rd). Afterwards, they take the bottle to the present where they wish Vegeta out of the bottle with the Earth Dragon Balls and then seal Zamasu's bottle in the RoSaT before destroying the entrance to prevent any possibility of his release once Beerus reveals that he can't erase an immortal. Afterwards, Trunks sets off to his future where he frees the sealed Gowasu in Universe 9 and take off with him to find Zunama to restore the Super Dragon Balls so that the damage to his timeline can be restored, leaving things open-ended as to whether he will succeed.
[mention]ahill1[/mention] That's about the best I can think of at the moment since you created the thread without warning. Feel free to share your own version of the Future Trunks arc.