I feel that if you wanted to try and have a normal healthy 'boring' relationship with her, you went off the track already. I assume with 'hooking up' you mean like a sex-date.

You were apart, didn't see each other a lot. She dated other people. When together you explored sexuality. And you both made a conscious effort not to get too emotional involved? At least you did.
It seems to me that this set a lot of precedent and patterns that will make it even more difficult for her to settle into a more boring, traditional routine.

You have known each other quite a long time. You haven't become a team. You say you have a real connection. But at the same time you say you deliberately kept distance/avoided it from becoming a real relationship. And that dates were about sex, not emotional bonding. And you haven't been honest with her, and she probably not with you.

I guess that's quite a lot of bad signs you bring up. Now relationships aren't perfect. But if this is going to work, it sounds like it will be really difficult, filled with drama, lot's of highs and lows.