I think part of the issue is whether the belief that there was collusion was in good faith on the part of those who pursued it.
When you take a step back and see the entire picture, i.e. the fact that intelligence showed that Russia was in fact trying to influence things via social media, then add in shady folks like Manaforte and dumber folks line Flynn finding themselves in high ranking positions within the campaign, then add in Trump's seeming admiration for Putin, is it really any wonder that folks were suspicious that there was an organized collusion going on?
In retrospect, it looks more and more like Trump and his team were simply duped into it, manipulated by Russian intelligence and Putin. We can debate the degree of their knowing what was going on. But it is beyond debate that Russia was trying to get its hooks into Trump.
How is that remotely possible? Brennan warned Obama, DOJ/FBI, State in
July 26, 2016 the Clinton campaign was scheming to tie Trump to Russia to deflect from her email scandal. Carter Page was the October 2016 FISA gateway for them to conduct two-hop investigations into everyone in the campaign and administration. Not only did CIA expressly tell FBI that Page was a long-standing CHS, Page had assisted FBI with prosecuting Russian nationals in 2013. Yet, maligning him, ruining his business, reputation, and making him target of death threats wasn't enough; they had to falsify FISA applications. They blew past every cautionary flag, and knew in Jan 2017 the dossier was propaganda.
Russian propaganda. The investigation into the Trump campaign should have ended right there, and Mueller should have never been appointed in May 2017 since a SC is not needed to investigate Russian nationals.
But they pressed on despite knowing they'd no predicate except their expressed distaste and/or outright hatred of a Trump presidency. We see this in the disgraced senior officials who were forced out of the bureau for bias, perjury, illegal leaking, and usurpation of DOJ authority. We see it in the glaring omissions of exculpatory evidence re: Pappadopoulos, Page, Flynn, etc.
Let's take two of your examples. Manafort and C. Kilimnik were trusted operators
for the Obama WH and U.S. government a decade prior; they went to great lengths to protect Kilimnik as a source and facilitator. But when Manafort become part of the campaign, suddenly he's a Russian colluder and Kilimnik is painted as a Russian intel officer - WTF? Comey and Mueller both knew better but emphasized the 'Russiaaaaaahh!' while obscuring everything else about them that said "nope, not Russia". They repeated this pattern over and over again. If a contact had beluga caviar for brunch, never mind they had decades involvement with Western intel; ignore that and go with the Russian fish eggs.
It's why IG Horowitz, FISC judge James Boasberg, AG Barr, and anyone concerned with the law and agency corruption have commented forcefully regarding the pattern, noting there is no explanation for these probes malfeasance and malevolence, given with the highest visibility possible from senior-most positions. It's why AGs Yates and Rosenstein say they would not have signed off on the FISA applications if aware of FBI's bad faith and illegality.
Russians didn't dupe or manipulate them; American agencies with agenda decided Trump was unacceptable and they would "stop it" and when they didn't, they reverted to the "insurance policy".
How was Russian "trying to get it's hooks into Trump" and why, if they actually thought that, did the Obama admin not give Trump a defensive briefing? Flynn's not a "dumb" guy, yet Comey thought "hey, let's NOT do what is customary and set up a meeting with Flynn and legal reps, let's DO show up as common friends and try to entrap". Flynn was financially ruined after serving the country for decades at a high level, by going after his family and disregarding agents telling Comey they guy made no attempt to mislead.
This is why I wish the same rogue, bureaucratic harm fall on people who won't see past Trump to the real danger. It isn't Russia, not China - and certainly not Trump - but our own corrupt, lawless bureaucracy. If they can do this to a president and damn near get him, and suffer no consequences nor be accountable to anyone, then everyone's life and liberty is subject to a Kafkaesque whim of the state. Some people have to be eaten by the lion to stop associating it with their house cat.