That doesn't sound nuts at all; in fact, it was my first thought, that you're confronted with the fact that this *particular* man smells "wrong" to you on the subconscious level. In other words, it seems possible that it's not as pervasive or offensive *to everyone else* as you perceive it. That's not saying you're making it up, but rather that it's a fundamentally incompatible scent for your particular brain/preferences/whatever. I've known people like that, who didn't smell strongly or bad (and who found plenty of dates!) but whose personal scent made ME kind of ill. Which sucks - usually we filter out people like that after the first date, but in this case you'd already fallen in love with him long beforehand.
There's even some research suggesting that women who are on the Pill react differently to personal scents than they do when they aren't taking hormonal medication, and in some cases they go off of it and find their partner suddenly smells "wrong" and not-desirable, so there's precedent for this. Doesn't make it any less awful, though.
For me, I found my wife's previous smell appealing and the same is true of her on-HRT smell, but they ARE different. Even though I don't dislike the new scent, it took me probably months to get over this hindbrain reaction that there was a stranger living in my house, b/c she didn't smell right. I minded it more than our cats did, for heaven's sake.
I'm afraid I don't have any useful suggestions beyond patience and hoping that as his body chemistry settles down it straightens out, but I wanted you to know you're not crazy or alone in this.