Welcome to the forum! Just so you know, as a moderator I'm going to remove your last name from your post just in case it can be used to identify you. Unfortunately, employers and other people might do a search on your name and find out things you'd rather they not know.
I prefer to treat such situations as hypothetical, because although you've laid out a certain amount of information, you haven't told every single thing, and neither should you. You don't want all your information to be all over the place.
If it were me, I would find out about things like incubation periods and possible dormant cycles for the disease in question. I'm under the impression that some can take a while. I don't know about three years, but I haven't studied any in depth. I would make sure my partner has been tested for the disease in question. Whatever the outcome of our relationship, it's important that he look into that. If both partners have had past relationships where such things could come into play, it could have been dormant in either person and blame is a bit silly. However it came to happen, both need to deal with it now and how they choose to do that will define how the marriage proceeds.
For more specific issues of what one should and should not do, I would find a priest who can give good advice that's faithful to the Magisterium. There's going to be a painful honest moment about the fact that since the couple hasn't been married in the Church, they're not really married, but most of the priests I know will look at the couple's intention to make things right with Our Lord and work on how to get them there.
Saying a prayer that you will receive the prudence you need to work through this.
"May God help us not to spoil His work" (Bl. Mother Theresa)