Scott88, while I was out running just now, I came up with the same thoughts you have on this. I think I've been overthinking this one a bit. I think it's likely that after she realized who Ennis was that she simply made the connection, as you say, about Jack's trips and Jack's desire to be with Ennis.
Wayne, my thought is that Lureen is telling Ennis about going up to the ranch in keeping with this other wish...so she is referring to Ennis, not anyone else. If she were thinking of R, it doesn't seem she would allude to this other wish while talking with Ennis. She naturally makes the connection to Ennis because she knows now Jack's wish was to be with him. I'm still unsure how much she knows about his murder, but I wouldn't rule out that she knows something about it, perhaps after the fact.