I'm going to be blunt about my first reactions to some of what you wrote, hopefully it doesn't come across as harsh but I am hoping that you will take some time to really reflect on what is going on. It kind of is a sore spot with me when somebody thinks they don't have the "right" to ask for whatever they want. Getting it isnt always possible, but asking for it should be encouraged by everybody.
1. So the wife can read any of your correspondence. Does she read all of your correspondence? Some people do have this policy, so it's good at least that you know about it. I will look at something written to my husband when he seems confused and says "this is the situation I think" and I've gotten the idea he got it all wrong, and I've had him read a message to me so I can tell him if I think he is off base. I do expect him to disclose to his partners that he may bounce everything off of me as I'm his friend, but if they want privacy about some things that's fine, if they want a DADT policy where i get to know nothing about them, well thats not comfortable with me and would require some negotiation. I am more likely to ask more questions in a new relationship too. However, you have been seeing each other for a long time (not that thats actually relevant). You know you can ask that you start getting some privacy on that? The wife knows you, has been able to have personal access to your behavior and words, and if she's still vigilant on what is being said, that leads me to believe their relationship probably has some serious issues if you cant say its time to respect your desire for privacy and you cant have it. If that is the case it does not sound like she is ready for or open to being poly.
Disclosure is different for everybody. My husband is OK if I talk about his stuff so I do if I have a reason to (on this forum or to friends). My boyfriend seems private, so although I may discuss some things happening between him and I, I try to err on the side of not talking about it. If my husband asked for information I wasn't sure about the privacy level of, preferably I'd run it by my bf first (and certainly would if it didn't have any impact on my husband), if not I'd let him know I'd shared something the next time I saw him. My husband is welcome to ask to see what I
am saying to people in email or messages (though I can't imagine him doing so) and if he asked I'd warn him if he was going to see something he'd rather not. I don't save my IM's, so there's nothing to be looked at, I wouldn't start just so they could be looked at by my spouse though.
If she is looking through your messages after this long, she should probably be spending that free time working on her self esteem.
I had a lot more to say but I started this a few hours ago then ended up going out and having a few beers so I think I'll wait to say anything else.
edit - couldn't resist. This forced sharing of your every thought with a third party sounds like a forced triad to me still. Would be a good point to bring up if you want to discuss the subject.