Re: red flags everywhere or am I crazy?
For sure your trust in her is shot. That is the primary problem to you remaining married or having a happy marriage. As I said before, her story is plausible. It may or may not be probable, but I've known people who are weak and naive as your wife is presenting. The problem is the red flags are based on logic and human experience, which is why so many are jumping to the conclusion she obviously cheated.
So you have a few choices here. One is to simply say the breach in the marriage is sufficient to justify divorce regardless of whether she actually had sex with the guy. Another choice would be to investigate to get as much information as possible in order to determine if she had an affair with him. The third choice is to accept she did cheat, and that you are willing to truly forgive it and move forward in the marriage.
I don't think the 3rd choice will work for you. It isn't rug-sweeping because you would accept the situation as she did have an affair. But you would simply put it in the past and move forward. You don't sound like the kind who could do that.
The first option is a possibility. But, like many, you have complications which make it an undesirable outcome. I think you said you have kids, but I could be confusing threads. If there are no kids, divorce may be an option to get to a happier place.
But I like Option 2, which is to investigate. Since all of this is past history with no suspected continuing affair, it may be more difficult. But, she may well be in contact with friends, family, or even the man in question. She may be discussing the situation with people. So you have a small window here to catch her comms. VAR the car and VAR a room in the house where she makes regular voice calls. Keylog the family computer if she uses it. Use the phone recovery tools people have suggested. Look at recovering backups of her phone to the computer. Recover emails from her deleted folder on her phone, computer, and tablet.
In a week you should have all of this data.
If there is still no strong proof in one direction or the other, do the polygraph. I think it is an extreme measure, but she has definitely done things which raise suspicions in a reasonable adult. A polygraph can undermine her sense of security in the relationship, so I would put it as a last resort.
But the fact is if you cannot establish trust in the marriage then your marriage will eventually fail. The issue isn't really whether she had an affair with the guy, it is whether you can have a good happy marriage with her. That requires trust.