I just fiddled around with it a little. Looks like the problem of the companion wheel and follower dialogue not showing up is because I was using a female PC. When I player.sexchanged and tried hiring her again the game considered her to be a proper follower. I'd say there's a difference in the scripts under the GREETING dialogue topic in FollowersHireClover quest.
However, regardless of gender she refuses to use any package except standing on Eulogy's balcony and smoking. Wherever I fast-travel to, she shows up next to me and then starts walking back to Eulogy.
I'm fairly sure none of my mods edit anything that could cause this, so can anybody confirm this happens?
edit ; I fixed this. Some of Clover's greeting to females referenced butch instead of clover so I fixed that, then I put some Followers.CloverHired == 0 conditions on her non-follower AI packages. I'm not sure if that's the ideal way of fixing it but it's been working okay for me so far. Here's my bugfix esp if anyone wants to merge this in.