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Not sure what you mean when you say "keep the three factions minus the institute" the Institute is the third of four factions. Minutemen are the 'default value'.
You don't have to destroy anyone else if you don't want to, after the institute or the blimp are destroyed, really.
There is a major mod - I do not know whether it's been updated to work with the next gen update, because it's *very* script heavy and requires f4se - called SUBVERSION which has a very intricate, and kinda fiddly and tough to slog through - full "everyone actually remains and YOU ARE the actual leader of the commonwealth" mod.
1) You do The Brotherhood missions right up to the point where they try to give you the quest called Tactical Thinking, you'll usually get it after Blind Betrayal, so as soon as you've sorted things out with Danse simply never speak to Kells again and you'll be fine.
2) For The Railroad do all missions up until Underground Undercover, You can do part of Underground Undercover up until a certain point as the Railroad and Institute missions overlap at this point.
3) For The Institute do all the missions up until The Battle of Bunker Hill.
This is important.
When you get the mission, inform The Railroad of what you've been asked to do and you'll be given an optional mission to free the synths instead of reclaiming them for The Institute.
Begin Battle of Bunker Hill, it's fine to kill Brotherhood members who are attacking The Railroad if they get in your way or put the synths in danger, you won't go hostile with The Brotherhood.
Reach the synths and free them.
4) Return to Father and use all the negative/aggressive speech options until you pith him off, which causes him to banish you from The Institute. This will begin the mission 'Banished from The Institute.
5) The mission called Form Ranks will now begin, where you'll have to defend The Castle. Hopefully you've already built plenty of defence and missile towers at this point.
Fight off the Institute attack, and afterward you can begin The Nuclear Option with The Minutemen.
It's VITAL to use the computer terminal in Father's office to evacuate the civilians and free the synths before blowing The Institute up, else you'll go hostile with The Railroad, and Preston will be severely upset with you.
And that's it.
There is a way to wipe out the Institute with BOS and still have the RR intact. But it requires using the console to finish Tactical Thinking before talking to the Captain. And actually, don't talk to him at all.
Do not kill RR members at Bunker Hill, if you have Deacon with you as a companion. I normally do not kill anyone during that quest except the Courser.
It is possible to rescue(?) some of the less-insane Institute scientists and some of the willing synths prior to the destruction of the Institute which will require being friends with the Institute while working for the BoS and RR.
As for a step-by-step guide? Yes. I know there are, but I couldn't point you to them. A search should turn up several of them with varying results on the outcomes.
This is correct. The normal and safe way.
The console command can make it so you can destroy the Institute with BOS and still keep the RR intact. You can still do quests not related to the Institute with the RR and even have Deacon as a companion.
I really think it is a bad game design to not give you the option to ignore the RR quest to cause them to become enemies and still get the option to wipe out the Institute.
But I don't recommend using the console unless you really know what you are doing. Using it incorrectly, can mess up your game. But if you do understand and are sure to save your game before using it, it is safe to use and extremely handy at times.
https://www.nexusmods.com/fallout4/mods/20330
It gives you the option to persuade Kells to spare The Railroad with a speech check.
It works, it's effective and I have tested it myself.
Yes. You can use mods like Ffabbia linked to above or in vanilla, there is a way to do it if you stop before certain quests and make particular choices in them. It takes a while to find the good one in all of the pointless chatty crap on Reddit, so here you go:
https://www.reddit.com/r/Fallout/comments/42965r/comprehensive_guide_to_not_destroying_factions_in/
And that option should have been in the game. For those who want to use mods, that sounds like a good one.