Cujo,
I think whether or not you choose to use a polygraph is up to you. From what I've read on polygraphs, polygraphs are more likely to get a truthful result when lying than to get a result of lying when telling the truth but I don't spend a lot of time researching polygraphs so there may be evidence to the contrary on that, too. The point is, it's your marriage and if this is what you need to feel safe in it, do what you need to do. In my opinion, your husband's willingness to take one says more than the actual results. Did he do it willingly or suggest he'd do it himself or was it with reluctance and under duress? If he wasn't chomping at the bit to do anything to prove he was being honest, that would have been your first clue that he was still lying. The response afterward is less telling than the willingness prior.
What is more important than the polygraph results and the subsequent information that he was, in fact, still lying is that you know your husband. You may think you don't know him right now but, deep down, you do.
If your spouse tells you a story that makes no sense, there is a 99% + chance he is LYING!
I don't know about 99% but this is probably the best indicator of deception or honesty that you will ever have. You know your husband. You know what makes sense based on what you know of him. You know how he behaves when he's taking responsibility for screwing up and you know how he behaves when he's still trying to cover his ass. If his behavior looks more like ass covering than taking responsibility, he's probably still trying to cover his ass.
As far as reconciliation goes, I've been here long enough to notice one pattern that is telling as far as reconciliation goes and it's with the wayward. If the wayward has a consistent pattern of taking responsibility for screw ups without blame-shifting in most areas of life: work, parenting, personal relationships, and all of this lying and blame-shifting are unusual, reconciliation is usually successful once the wayward recognizes his/her anomalous behavior and begins to behave in an honest and respectable way. But if your wayward has a history of blaming everyone else ("the boss has it in for me", "my teacher failed me", "she seduced me") when things go wrong instead of looking at his/her own contribution to the problem, this is just more of the same and the wayward is unlikely to suddenly become introspective and make real change. I'm not saying that this type of wayward can't change but a wayward who has never taken responsibility for his/her actions and has, instead, always found someone else to scapegoat has to dig very deep to figure out that this is actually a pattern that has to be changed.
So, if I were you, I'd take some time to myself and give some serious consideration to whether or not your husband has had a pattern of blame-shifting all of his life. Then consider how he has lied in the past. Is his go-to method of deflecting his lies to become indignant and defensive? If so, is his behavior after the polygraph more of the same? Do his stories line up with what you know of him as a person and how he would behave under the circumstances? Or do his stories seem illogical given what you know about him?
As long as anything doesn't make sense, you will continue to search for information that helps them make sense. You will not rest easy with a story that is illogical based on what you know of your husband. And that is whether or not he passes a polygraph. Even a passed polygraph will only help you rest easy temporarily if his stories still don't line up. So you should take some time to yourself to figure out what you want and what you need to feel safe if you reconcile with him. You will also have to come to terms with the fact that even if he has told you everything, you will never know every detail and what you do know will only ever be from his perspective which may be skewed. You will have to decide if you can move forward with what you have.
I will tell you that as long as my husband was behaving indignantly and defensively, he was still lying. It wasn't until he came completely clean that he could answer my questions calmly and with my healing in mind. As long as he was covering his ass, the conversations were heated and felt like teeth-pulling. On the day he told me everything, with his shoulders dropped in resignation, all of that stopped. And once he came clean, any new questions were answered with a resigned yes or no. He stopped fighting to protect himself and his image and started protecting me. And he understood why I needed to ask the same questions over and over. He knew that he's put so many questions in my mind that it would take a long time to feel secure that I knew everything and that he was now behaving as a husband should. And he developed boundaries with women and worked on his conflict avoidance because he recognized that his boundaries and coping skills were very poor.
So sit down and ask yourself some questions about your husband. Is blame-shifting and avoiding responsibility for wrong doing new or has he done this consistently in other areas of life? Does he have a history of poor boundaries with women and, if so, is he willing to develop better boundaries? Has he always had to have his ego boosted by flirting and attention from women or his ego less fragile and based more strongly in his abilities and temperament and less in external validation? Do his stories make sense given what you know about him as a person or do you feel that it still isn't lining up? If the stories don't make sense, what information makes better sense to you (because that is likely what actually happened) and can you live with it if he were to admit to it? Is he willing to do anything to help make you feel safe continuing the marriage? And what exactly would you need to make you feel safe continuing the marriage?
The answers you get from asking and answering those questions are your starting point for moving forward. When we are betrayed, we feel like our spouse has all the power but, in reality, you actually have a great deal of power. Whether or not you choose to give him a chance to reconcile is up to you. Whether or not he chooses to accept that chance for the gift that it is and do everything he can to earn it is up to him.