I find myself here this morning, 3 years after discovering my husband and closest friend at the time had been together sexually. He swears it was only one time. He refuses to talk about it. 
After the shock wore off things started popping into my memory. My Autistic son walked right up to her in my kitchen and told her that his mom and dad were together, and that she needed to know that. She swore she would never do anything like that. Me being who I was then, laughed it off. 
I also discovered that he was signed into my sons computer, so I looked on his Google maps history. There were time stops at her home, and at most of the places she had been working. Which he denied completely. 
She sent him text messages, and he showed me. But when I asked him why she wasn’t blocked and why he responded to her without saying, anything about it not being right because he is married and he “loves” me. His response was that he didn’t want her to be angry towards him. She could ruin our lives. I think now he is more afraid of what I will find out. 
Then when he went to bed, I looked through his phone. Her name was in the search history, in Facebook search, and Linked in. Which he said I put there to try to punish him with. 
He ran into her more than once and never mentioned it. A girlfriend of mine asked him in front of me who he was talking to in the store. Again I was the reason he didn’t tell me. He didn’t want me yelling at him for talking to her. 
Other little things, glances, touches on the back, walking her out to her car every time she left. Once he knew I bumped into her physically in town. I was not going to say anything but when I got home he was grilling me, where were you? What have you been doing. He knew I was getting my hair cut. When I said you don’t even want to know who I saw, he said “I Know” and when I looked at him he said you know you get those feelings. No possible way he could have known I saw her. 
I dug and searched, there were things here and there but nothing concrete. We fought terribly for two years, almost to the point of divorce. But he would never admit anything more. I was so consumed with finding an answer. I was going crazy. Then I made up my mind. I just stopped. 
After a few months I looked in his phone once more. And in the google history is her address looked up in August before I found out in December. That to me was the proof I needed. Why would he need to look up her address. I haven’t said anything. In fact I have not mentioned her in almost a year now.
why I am writing is suddenly my gut is talking to me. Something is not right. And my husband is a mess. He had to take a 3 month leave of absence from work, he off and on binge drinks, he picks fights, with his parents, me, my oldest son. 
He swore he would tell me if he ever saw her again. I think he has. In a bar he was at with his friends. There are just things I can’t explain. 
So my question is, will he ever tell me? Should I tell him I know for sure he was with her more than once. And if not, will these horrible gut feelings keep coming back and haunting me. I am trapped in them right now, I need to break free. I need help.
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Gosh, that is an incredibly painful place to be. 

I look back and see how I was tortured with suspicion but somehow I just kept blocking it because my wife had looked me in the eye and said, "just friends". I mean, it is insane in retrospect but I believed her even while some deep down part of me knew it was mad. So that split inside me was torture itself though I didn't understand it at the time.

Your husband is reacting with anger instead of helping you with understandable pain. He is failing you on that level even if that is all it is. But you are right, I think, those behaviours you are describing of picking fights and drinking are all too consistent with an affair to ignore, and there is clearly history there. 

Some people think they can lie their way out of it, as though life is a series of episodes like a TV show and as long as they manage to fool you in season three, episode four it just won't come up again in season six. So your husband thinks he can lie and as long as the lie works it will be okay. 

Your questions: It does not sound like he will tell you on his own. Yes, the horrible gut feelings will keep coming back. 

Should you tell him what you know for sure? I don't think so. I think that you should tell him you are giving him a chance now to come clean with everything, that you know more than he realises, and that if he isn't honest now your marriage is in deep jeopardy that it might not come back from.

Then listen. He will say, "what do you actually know???" and you will say, "never mind what I know, tell me everything now." (Otherwise he will just lie enough to address that one thing.) And then if he sticks to the "just one time" story you will know he is still lying. And then do your best to say, "okay, is that really the best you can do?", and then go be by yourself and think about what to do next. 

Those are just my thoughts, there is no right answer and your gut is your best guide. 

Good luck, I know what you are feeling.
Maybe it is okay, maybe it will be okay.

BS, d-day Feb 2017, 16 mth affair.
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By the way, here's a true story. It would be funny if it weren't so serious. 

My wife's AP expressly told her that if they were ever confronted about the affair, they should simply deny it. Nobody could prove it so deny, deny, deny. Then she confessed to me because she couldn't stand the lying any more. So for about two weeks I knew but the AP's wife did not.

Then one night, just when my wife and I had had a really good day (all things considered)... someone sent the AP's wife an anonymous message via linkedin, telling her about the affair. She showed it to him and said, "is this true?" He admitted it because he thought I had sent it

I hadn't sent it, in fact it threw my life into disarray and seemed like a disaster to me (it probably wasn't, but it certainly made for a hard few months). But because he thought there was "proof" now (ie my knowledge) he confessed. If the same message had come before I knew about the affair, he'd have lied through his teeth about it.

I am telling this story because:

(a) people who get caught up in lying can actually specifically think, "I will just lie and lie and lie and that's a good strategy."
(b) if you tell him what you know, he can actually think, "I just need to come up with the right lie to deal with that one thing."
Maybe it is okay, maybe it will be okay.

BS, d-day Feb 2017, 16 mth affair.
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Agreed.  Definitely do not tell him what you know.  Just that you know he's lying.  And then give him the choice to either confess or not, but I would make it clear to him that you will not tolerate any more lies.  

Nonetheless, he'll probably continue to lie because, as anthropoidape said, lying has become his new normal, and his go to escape route for whatever threatens him.  You'll then have to decide what you want to do.  And be willing to do it, because otherwise, he'll have no reason to seriously consider his choice in that regard. 
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you wrote:
So my question is, will he ever tell me? Should I tell him I know for sure he was with her more than once. And if not, will these horrible gut feelings keep coming back and haunting me. I am trapped in them right now, I need to break free. I need help.
I would like to suggest that the better question is: Is this behavior acceptable to me from my partner?  Is this the marriage I signed up for, or has my WS decided to unilaterally (and secretly) change the terms of engagement?
How do YOU demand to be treated?  are you willing to be lied to? "What you allow is what will continue"
I suggest that you start focusing on YOU and YOUR worth.
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