I also recently got to 40, first 6 months of legendaries I saw the importance of taking two to 30+. Doubles of Raikou, Moltres, Lugia, Mewtwo (4). However, past month I finished maxing a Raikou, Mewtwo, and Kyogre. I also transferred quite a lot of 80% legendaries today and will put that candy into my best one. I'd say put yours into the higher level Raikou and Rayquaza.
Lugia and Ho-oh more of a player judgment call--I actually have a 3300 and a 3125 Lugia, so I'm not one to say it is a no-brainer to have one 3500+, however, most would say focus on one--especially since a luxury/niche