In that context, prior to the January 6 meeting, I discussed with the FBI’s leadership team whether I should be prepared to assure President-Elect Trump that we were not investigating him personally. That was true; we did not have an open counter-intelligence case on him. We agreed I should do so if circumstances warranted. During our one-on-one meeting at Trump Tower, based on President- Elect Trump’s reaction to the briefing and without him directly asking the question, I offered that assurance.
As of January 6, 2017 Donald Trump was not the subject of a counterintelligence investigation, and Comey notified him as much.
My instincts told me that the one-on-one setting, and the pretense that this was our first discussion about my position, meant the dinner was, at least in part, an effort to have me ask for my job and create some sort of patronage relationship. That concerned me greatly, given the FBI’s traditionally independent status in the executive branch. . .
Near the end of our dinner, the President returned to the subject of my job . . . A few moments later, the President said, “I need loyalty, I expect loyalty.” . . .
He then said, “I need loyalty.” I replied, “You will always get honesty from me.” He paused and then said, “That’s what I want, honest loyalty.” I paused, and then said, “You will get that from me.”
January 27, Trump attempts to establish a "patronage relationship" and demands loyalty.
When the door by the grandfather clock closed, and we were alone, the President began by saying, “I want to talk about Mike Flynn.” Flynn had resigned the previous day. The President began by saying Flynn hadn’t done anything wrong in speaking with the Russians, but he had to let him go because he had misled the Vice President. He added that he had other concerns about Flynn, which he did not then specify.
The President then returned to the topic of Mike Flynn, saying, “He is a good guy and has been through a lot.” He repeated that Flynn hadn’t done anything wrong on his calls with the Russians, but had misled the Vice President. He then said, “I hope you can see your way clear to letting this go, to letting Flynn go."
I immediately prepared an unclassified memo of the conversation about Flynn and discussed the matter with FBI senior leadership. . . Regardless, it was very concerning, given the FBI’s role as an independent investigative agency.
February 14, the President requests Comey drop the investigation into Michael Flynn.
On the morning of March 30, the President called me at the FBI. He described the Russia investigation as “a cloud” that was impairing his ability to act on behalf of the country. He said he had nothing to do with Russia, had not been involved with hookers in Russia, and had always assumed he was being recorded when in Russia. He asked what we could do to “lift the cloud.” I responded that we were investigating the matter as quickly as we could, and that there would be great benefit, if we didn’t find anything, to our having done the work well. He agreed, but then re-emphasized the problems this was causing him.
He finished by stressing “the cloud” that was interfering with his ability to make deals for the country and said he hoped I could find a way to get out that he wasn’t being investigated.
March 30, President Trump requests that Director Comey "Lift the Cloud" of the Russian investigation.
He said he would do that and added, “Because I have been very loyal to you, very loyal; we had that thing you know.” I did not reply or ask him what he meant by “that thing.” . . . That was the last time I spoke with President Trump.
April 11, the last time Comey spoke to President Trump.
TLDR - Trump was not, at least as of April 11, the subject of a counterintelligence investigation. Associates of Donald Trump's are the subject of a counterintelligence investigation, Congress knows who they are. Donald Trump pressured Comey to end the investigation into Flynn for the phone calls during the Transition. Repeatedly asked Comey to lift the cloud of the investigation.
Keep in mind, while these memos state that Comey does not seem to believe the actions amounted to obstruction of justice as of March 2017, much has happened since that time, the most significant of which is probably Comey's firing. Taken together, these statements and the subsequent actions may constitute obstruction of justice. Even though Trump was not the subject of a counterintelligence investigation, it is clear many of his associates are, and he may have been attempting to protect them, or himself.
edit - I feel like the balance of "your not going far enough" regarding obstruction of justice in your summary versus "you are going to far" in the comments I am getting suggests I may have gotten it about right ;)